A comparison of nasopharyngeal and oropharyngeal swabbing for the detection of influenza virus by real-time PCR

Difference between real world practice and clinical research: A comparison of oropharyngeal and nasopharyngeal sampling data in influenza

Oropharyngeal (OP) sampling is one of the most commonly used methods for respiratory sampling, but its positivity rate in real practice compared with that of nasopharyngeal (NP) sampling is not fully known. The differences between OP and NP in practice and between practice and the literature were compared. In total, 2323 positive results from 6708 patients were recorded in the laboratory test system, and 15,021 positive results from 31,333 patients were recorded in the national report. The positivity rate changed from 2.3 % to 38.11 % after the sampling method was changed from OP to NP in the same setting. The difference between OP and NP (calculated as (NP-OP)/NP) varies from -7.73-28.57 % in the literature and from 61.35-94.59 % in practice. Real-world practice is complicated and thus different from strictly quality-controlled studies.

A SARS-CoV-2 and influenza rapid antigen test-based hospital isolation policy awaiting RT-PCR, a prospective observational study

OBJECTIVES

This study aimed to evaluate the clinical performance of a combined SARS-CoV-2/influenza rapid antigen test (SIRAT) and to evaluate a SIRAT-based hospital isolation policy awaiting RT-PCR results for patients presenting at the emergency department (ED).

METHODS

We performed a prospective observational study including all adult patients presenting with influenza-like symptoms at the ED of two hospitals from 31 October 2022 to 31 March 2023. A SIRAT and SARS-CoV-2 and influenza RT-PCR were performed on upper respiratory samples. SIRAT results were compared with RT-PCR. Droplet and contact isolation measures (DCIM) were imposed based on SIRAT results awaiting RT-PCR. We monitored symptomatic nosocomial SARS-CoV-2 and influenza infections potentially caused by delayed isolation of patients with false negative SIRAT and the hours of unnecessary DCIM saved.

RESULTS

We included 1740 patients of whom 1296 were hospitalized. SARS-CoV-2 and influenza A/B prevalence were 12.7% (221/1740) and 9.9% (171/1740). Sensitivity and specificity of the SIRAT were 67.7% (95% CI 61.1-73.9%) (149/220) and 99.4% (95% CI 99.0-99.8%) (1510/1518) for SARS-CoV-2 and 52.7% (95% CI 44.9-60.4%) (89/169) and 99.1% (95% CI 98.5-99.5%) (1530/1544) for influenza A/B. We found a 0% nosocomial transmission risk for SARS-CoV-2 (95% CI 0-8.8%) and influenza (95% CI 0-10%). In all, 8712 hours in total or a median up to 6 hours 59 minutes (IQR (interquartile range) 11h03) per patient of unnecessary DCIM were saved.

DISCUSSION

A SIRAT-guided hospital isolation policy awaiting RT-PCR results for patients who present at the ED can save unnecessary isolation hours without having to lead to significant symptomatic nosocomial transmission of SARS-CoV-2 or influenza viruses.

Comparing SARS-CoV-2 Testing in Anterior Nasal Vestibular Swabs vs. Oropharyngeal Swabs

Purpose

To investigate the sensitivity of SARS-CoV-2 testing in specimens collected from the anterior nasal vestibules of COVID-19 patients.

Methods

A cross-sectional analysis was performed on 30 patients with a confirmed diagnosis of COVID-19 at the Shanghai Public Health Clinical Center from March 14, 2020 to March 21, 2020. Paired specimens were collected from both the anterior nasal vestibule and the oropharynx from all patients. All specimens were tested for SARS-CoV-2 using reverse transcription-polymerase chain reaction (RT-PCR) assays.

Results

Of the 30 patients with confirmed COVID-19, 17 patients (56.7%) tested positive for SARS-CoV-2 when oropharyngeal specimens were used, while 20 patients (66.7%) tested positive when nasal swab specimens were used. There was no statistically significant difference in sensitivity between the two methods.

Conclusions

Respiratory swabs collected from the nasal vestibule offer a less invasive alternative to oropharyngeal swabs for specimen collection in the detection of SARS-CoV-2 infection, and have adequate sensitivity.

Covid-19 and ENT practice: Our experience: ENT outpatient department, ward and operating room management during the SARS-CoV-2 pandemic

Objectives

The current study aims at assessing the effectiveness of the guidelines set up by our clinic for the protection of patients and staff which enabled us to proceed with urgent and oncological surgery after the outbreak of the Covid-19 pandemic.

Material and methods

Our ENT department devised specific equipment to be worn by the staff for personal protection when dealing with Covid-19 patients both in aerosol generating and non-generating procedures. Moreover, restrictive measures were enforced both for the outpatient department and for the ward where only urgent practices were carried out and visitors were not allowed, while non-urgent elective surgery was postponed. A codified scheme was followed to perform tracheostomy procedure in Covid-19 positive testing patients on the part of 3 specific teams of 2 surgeons each, while the resident educational program was reorganized to limit the spread of the infection.

Results

In about a couple of months (from March 8th to May 3rd) a relevant amount of medical tests and surgical procedures were carried out on non COVID-19 patients and a certain number of tracheostomies were performed on COVID-19 patients. Consequently, all the ENT personnel were checked and found negative. Also, all the patients in the ward were swab tested and chest X-rayed, only one had a positive outcome and was adequately handled and treated.

Conclusion

Our ENT guidelines regarding personal protection equipment and multiple simultaneous diagnostic procedures have proved to be an essential instrument for the management of patients with both known and unknown COVID-19 status.

Cost evaluation of point-of-care testing for community-acquired influenza in adults presenting to the emergency department

BACKGROUND

Rapid molecular point-of-care tests (POCTs) for influenza have potential to produce cost savings in emergency departments (EDs) and acute care settings. To date, published projected savings have been based on estimated costs.

OBJECTIVES

This study aimed to describe the cost implications of a rapid influenza POCT using accurate real-world patient level costing data. 204 adult patients receiving point-of-care (POC) influenza testing in the ED as part of a routine clinical service were identified retrospectively, alongside a control cohort of 104 patients from the same influenza season. Costs for all were calculated at the individual patient level. Cost comparison was performed using an instrumental variable (IV) regression to overcome potential bias within the observational dataset.

RESULTS

Patients who had a POCT on average cost 67 % less than those who did not (average cost reduction: £2066: 95 % CI: £624 and £2665). Moderate to high NEWS score at arrival, presence of ≥1 comorbidity, and age ≥70 years increased overall costs across both groups (p < 0.05).

CONCLUSIONS

Savings from POC testing can be attributed to more targeted treatments, fewer admissions and reduced lengths of stay. The IV regression results are supported by a second method (ordinary least square against baseline characteristics). They are also in line with existing work that use estimated costs but indicate greater savings than predicted previously. In conclusion, POC influenza testing in the emergency department produces significant cost savings, this is demonstrated here through an analysis using individual real-world patient level costing data.

Nasopharyngeal Swabs Are More Sensitive Than Oropharyngeal Swabs for COVID-19 Diagnosis and Monitoring the SARS-CoV-2 Load

Objective: Detection of SARS-CoV-2 by oropharyngeal swabs (OPS) and nasopharyngeal swabs (NPS) is an essential method for coronavirus disease 2019 (COVID-19) management. It is not clear how detection rate, sensitivity, and the risk of exposure for medical providers differ in two sampling methods.

Methods: In this prospective study, 120 paired NPS and OPS specimens were collected from 120 inpatients with confirmed COVID-19. SARS-CoV-2 nucleic acid in swabs were detected by real-time RT-PCR. The SARS-CoV-2 detection rate, sensitivity, and viral load were analyzed with regards NPS and OPS. Sampling discomfort reported by patients was evaluated.

Results: The SARS-CoV-2 detection rate was significantly higher for NPS [46.7% (56/120)] than OPS [10.0% (12/120)] (P < 0.001). The sensitivity of NPS was also significantly higher than that of OPS (P < 0.001). At the time of sampling, the time of detectable SARS-CoV-2 had a longer median duration (25.0 vs. 20.5 days, respectively) and a longer maximum duration (41 vs. 39 days, respectively) in NPS than OPS. The mean cycle threshold (Ct) value of NPS (37.8, 95% CI: 37.0–38.6) was significantly lower than that of OPS (39.4, 95% CI: 38.9–39.8) by 1.6 (95% CI 1.0–2.2, P < 0.001), indicating that the SARS-CoV-2 load was significantly higher in NPS specimens than OPS. Patient discomfort was low in both sampling methods. During NPS sampling, patients were significantly less likely to have nausea and vomit.

Conclusions: NPS had significantly higher SARS-CoV-2 detection rate, sensitivity, and viral load than OPS. NPS could reduce droplets production during swabs. NPS should be recommended for diagnosing COVID-19 and monitoring SARS-CoV-2 load.

Chinese Clinical Trial Registry, number: ChiCTR2000029883.

Pathogens Causing Respiratory Tract Infections in Children Less Than 5 Years of Age in Senegal

Introduction:

While acute respiratory tract infections are the main cause of paediatric mortality and morbidity worldwide, pathogen patterns shift due to factors such as hygiene, vaccinations, and antibiotic resistance. Knowledge about current cause of respiratory infections is lacking, particularly in low- and middle-income countries. The aim of this study was to identity the various respiratory pathogens causing acute respiratory tract infections in children below 5 years of age visiting a sub-urban primary care clinic in Senegal.

Methods:

A case-control study was performed in September and October 2018. Oropharyngeal swabs were collected from cases; infants with fever and respiratory symptoms, and controls; children involved in the vaccination programme. Viral identification was conducted by polymerase chain reaction for 21 different viruses; bacteria were identified by culture studies. Associations between microorganisms, acute respiratory infection and severity of disease were calculated by multivariate regression adjusting for confounders such as age, sex, and living area.

Results:

Overall, 102 cases and 96 controls were included. Microorganisms were detected in 90.1% of cases and 53.7% of controls (P < .001). Influenza virus A (including H1N1), influenza virus B, respiratory syncytial virus (RSV), and Streptococcus pneumoniae were independently associated with acute respiratory tract infections. Co-detection of two or more pathogens was present in 49.5% of cases; 31.7% of cases had a pneumonia and 90.2% was treated with antibiotics.

Conclusions:

This case-control study in a primary care setting in sub-Saharan Africa found influenza virus A and B, RSV, and S pneumoniae to be the main causes of acute respiratory tract infections in children below 5 years of age. We recommend evaluation of antibiotics prescription behaviour in this setting.

Comparison of Respiratory Specimen Collection Methods for Detection of Influenza Virus Infection by Reverse Transcription-PCR: a Literature Review

The detection of influenza virus in respiratory specimens from ill individuals is the most commonly used method to identify influenza virus infection. A number of respiratory specimen types may be used, including swabs, brush, aspirate, and wash, and specimens may be collected from numerous sites, including the anterior and posterior nasopharynx, oropharynx, and nares. Traditionally, respiratory specimens from the nasopharynx have been considered to have the highest sensitivity for viral detection. However, as molecular assays such as reverse transcription-PCR (RT-PCR) have increased the sensitivity of viral detection from respiratory specimens, the use of less-invasive and easier-to-obtain specimens has increased for the detection of influenza virus. This review presents and evaluates the sensitivities of respiratory specimen methods used in epidemiologic studies that used RT-PCR to detect influenza virus in respiratory specimens from ill patients. This literature review suggested that a combination of two less-invasive swabbing methods, such as nasal and oropharyngeal swabs, had about the same sensitivity as did nasopharyngeal specimens for influenza virus detection by RT-PCR. By combining two less-invasive collection methods, it may be possible to reduce barriers to enrollment without compromising influenza virus detection sensitivity.

A combination of naso- and oropharyngeal swabs improves the diagnostic yield of respiratory viruses in adult emergency department patients

BACKGROUND

Along with the current development of molecular diagnostic methods of respiratory viruses, the bedside patient sampling techniques need to be evaluated. We here asked the question whether the addition of an oropharynx swab to the traditional nasopharynx swab might improve the diagnostic yield of multiplex PCR analysis. Ct values from the two sampling sites were compared as well as patient tolerability.

METHODS

In an emergency department in Malmö, Sweden, 98 adult patients with respiratory disease were sampled both from the nasopharynx and oropharynx for virus diagnostics by PCR.

RESULTS

Influenza (AH1, AH3, B), human metapneumovirus (hMPV) or respiratory syncytial virus (RSV) were detected by PCR in 58 subjects. The diagnostic yield was improved by combining nasopharyngeal and oropharyngeal sampling - a virus was detected in another 6 patients compared to traditional nasopharyngeal sampling (p = .031, McNemar's test). In 38/55 subjects viral load was higher in the nasopharynx than in the oropharynx. Self-reported discomfort was significantly lower from oropharyngeal sampling than from nasopharyngeal sampling.

CONCLUSIONS

Adding an oropharynx sample to a nasopharynx sample increased the diagnostic yield of respiratory viruses. Oropharyngeal sampling was well tolerated.

Accuracy of comprehensive PCR analysis of nasopharyngeal and oropharyngeal swabs for CT-scan-confirmed pneumonia in elderly patients: a prospective cohort study

OBJECTIVES

We aimed to assess the accuracy of PCR detection of viruses and bacteria on nasopharyngeal and oropharyngeal swabs (NPS) for the diagnosis of pneumonia in elderly individuals.

METHODS

We included consecutive hospitalized elderly individuals suspected of having pneumonia. At inclusion, NPS were collected from all participants and tested by PCR for the presence of viral and bacterial respiratory pathogens (index test, defined as comprehensive molecular testing). Routine diagnostic tests (blood and sputum culture, urine antigen detection) were also performed. The reference standard was the presence of pneumonia on a low-dose CT scan as assessed by two independent expert radiologists.

RESULTS

The diagnosis of pneumonia was confirmed in 127 of 199 (64%) included patients (mean age 83 years, community-acquired pneumonia in 105 (83%)). A pathogen was identified by comprehensive molecular testing in 114 patients (57%) and by routine methods in 22 (11%). Comprehensive molecular testing was positive for viruses in 62 patients (31%) and for bacteria in 73 (37%). The sensitivity and specificity were 61% (95% CI 53%-69%) and 50% (95% CI 39%-61%) for comprehensive molecular testing, and 14% (95% CI 82%-21%) and 94% (95% CI 86%-98%) for routine testing, respectively. Positive likelihood ratio was 2.55 for routine methods and 1.23 for comprehensive molecular testing.

CONCLUSION

Comprehensive molecular testing of NPS increases the number of pathogens detected compared with routine methods, but results are poorly predictive of the presence of pneumonia. Hence, comprehensive molecular testing is unlikely to impact clinical decision-making (NCT02467192).

CLINICAL TRIALS REGISTRATION

NCT02467192.

Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections

Respiratory viral infections are associated with a wide range of acute syndromes and infectious disease processes in children and adults worldwide. Many viruses are implicated in these infections, and these viruses are spread largely via respiratory means between humans but also occasionally from animals to humans. This article is an American Society for Microbiology (ASM)-sponsored Practical Guidance for Clinical Microbiology (PGCM) document identifying best practices for diagnosis and characterization of viruses that cause acute respiratory infections and replaces the most recent prior version of the ASM-sponsored Cumitech 21 document, Laboratory Diagnosis of Viral Respiratory Disease, published in 1986. The scope of the original document was quite broad, with an emphasis on clinical diagnosis of a wide variety of infectious agents and laboratory focus on antigen detection and viral culture. The new PGCM document is designed to be used by laboratorians in a wide variety of diagnostic and public health microbiology/virology laboratory settings worldwide. The article provides guidance to a rapidly changing field of diagnostics and outlines the epidemiology and clinical impact of acute respiratory viral infections, including preferred methods of specimen collection and current methods for diagnosis and characterization of viral pathogens causing acute respiratory tract infections. Compared to the case in 1986, molecular techniques are now the preferred diagnostic approaches for the detection of acute respiratory viruses, and they allow for automation, high-throughput workflows, and near-patient testing. These changes require quality assurance programs to prevent laboratory contamination as well as strong preanalytical screening approaches to utilize laboratory resources appropriately. Appropriate guidance from laboratorians to stakeholders will allow for appropriate specimen collection, as well as correct test ordering that will quickly identify highly transmissible emerging pathogens.

Influenza and respiratory syncytial virus screening for the detection of asymptomatically infected patients in hematology and oncology

Introduction: Respiratory syncytial virus (RSV) and influenza virus infections are a significant healthcare risk for immunocompromised patients. In addition to community onset, nosocomial acquisition and transmission may also occur. Detection of asymptomatic shedders (e.g., patients in the incubation period or immunosuppressed long term shedders) facilitates control of nosocomial transmission.

Methods: To strengthen the existing infection control concept, a PCR-based screening for RSV and influenza virus was implemented for all patients lacking respiratory symptoms (asymptomatic patients) who were hospitalized on an adult and a pediatric hemato-oncological ward. Laboratory results of this screening were analyzed retrospectively.

Results: 665 respiratory specimens were obtained for screening from 251 patients (26% were 18 years and younger) from December 2016 to April 2017. In 23 patients without respiratory symptoms, either influenza virus or RSV infection was found, resulting in a detection rate of about 9%. In 6 patients, the infection was presumably detected during the incubation period, because an increase of viral load was observed in subsequent specimens. Positive screening results facilitated timely implementation of adequate infection control precautions. Nosocomial clusters of RSV or influenza were not detected during the screening period on the two wards.

Conclusion: The seasonal screening program expanded our existing infection control concept in terms of patients lacking respiratory symptoms who shed influenza virus or RSV. It enabled us to identify 23 RSV or influenza infections in patients lacking respiratory symptoms in a 4-month period and thus to rapidly take isolation precautions.

Use of real-time semiquantitative PCR data in management of a neonatal intensive care unit adenovirus outbreak

OBJECTIVE

To describe an adenovirus outbreak in a neonatal intensive care unit (NICU), including the use of qualitative and semiquantitative real-time polymerase chain reaction (qPCR) data to inform the outbreak response.

DESIGN

Mixed prospective and retrospective observational study.

SETTING

A level IV NICU in the southeastern United States.PatientsTwo adenovirus cases were identified in a NICU. Screening of all inpatients with qPCR on nasopharyngeal specimens revealed 11 additional cases.InterventionsOutbreak response procedures, including enhanced infection control policies, were instituted. Serial qPCR studies were used to screen for new infections among exposed infants and to monitor viral clearance among cases. Changes to retinopathy of prematurity (ROP) exam procedures were made after an association was noted in those patients. At the end of the outbreak, a retrospective review allowed for comparison of clinical factors between the infected and uninfected groups.

RESULTS

There were no new cases among patients after outbreak identification. One adenovirus-infected patient died; the others recovered their clinical baselines. The ROP exams were associated with an increased risk of infection (odds ratio [OR], 84.6; 95% confidence interval [CI], 4.5-1,601). The duration of the outbreak response was 33 days, and the previously described second wave of cases after the end of the outbreak did not occur. Revisions to infection control policies remained in effect following the outbreak.

CONCLUSIONS

Retinopathy of prematurity exams are potential mechanisms of adenovirus transmission, and autoclaved or single-use instruments should be used to minimize this risk. Real-time molecular diagnostic and quantification data guided outbreak response procedures, which rapidly contained and fully terminated a NICU adenovirus outbreak.

What Is the Added Benefit of Oropharyngeal Swabs Compared to Nasal Swabs Alone for Respiratory Virus Detection in Hospitalized Children Aged <10 Years?

We evaluated the added value of collecting both nasal and oropharyngeal swabs, compared with collection of nasal swabs alone, for detection of common respiratory viruses by reverse transcription-polymerase chain reaction in hospitalized children aged <10 years. Nasal swabs had equal or greater sensitivity than oropharyngeal swabs for detection of respiratory syncytial virus, adenovirus, human metapneumovirus, rhinovirus, and influenza virus but not parainfluenza virus. The addition of an oropharyngeal swab, compared with use of a nasal swab alone, increased the frequency of detection of each respiratory virus by no more than 10% in children aged <10 years.