Collection Of Nasopharyngeal Specimens Research Articles

Comparison of the safety, effectiveness, and usability of swab robot vs. manual nasopharyngeal specimen collection

BackgroundHealthcare workers face a risk of infection during aerosol-generating procedures, such as nasal swabbing. Robot-assisted nasopharyngeal sampling aims to minimize this risk and reduce stress for healthcare providers. However, its effectiveness and safety require validation. MethodsWe conducted a controlled trial with 80 subjects at two teaching hospitals and compared robot-collected vs manually-collected nasopharyngeal swabs. The primary outcomes included specimen quality and success rate of nasopharyngeal swab collection. We also recorded the pain index, duration of the collection, and psychological stress using a post-collection questionnaire. ResultsDuring the study period, from September 23 to October 27, 2020, 40 subjects were enrolled in both the robotic and manual groups. The cycle threshold (Ct) value for nasopharyngeal specimens was statistically higher in the robotic group compared to the manual group (30.9 vs 28.0, p < 0.01). Both groups had Ct values under 35, indicating good quality specimens. In the robotic group, 3 out of 40 subjects required a second attempt at specimen collection, resulting in a success rate of 92.5 %. Further, although the pain levels were lower in the robotic group, the difference was not statistically significant (2.8 vs 3.6, p = 0.07). The manual group had a shorter sampling time, which was 29 s (201 vs 29, p < 0.05). However, when factoring in the time needed to put on personal protective equipment, the average time for the manual group increased to 251 s (201 vs 251, p < 0.05). Participants' questionnaire results show comparable psychological stress in both groups. Medical staff expressed that using a robot would reduce their psychological stress. ConclusionsWe propose a safe and effective robotic technology for collecting nasopharyngeal specimens without face-to-face contact, which may reduce the stress of physicians and nurses. This technology can also be optimized for efficiency, making it useful in situations where droplet-transmitted infectious diseases are a concern.

Paroxysmal Atrial Fibrillation with Rapid Ventricular Response Following COVID-19 Nasopharyngeal Swab: A Case Report

Nasopharyngeal (NP) swab sampling is a simple procedure that has become extremely popular in the coronavirus disease 2019 (COVID-19) era, with hundreds of million specimens collected every day. However, rare but serious complications have been reported following NP swab acquisition. Here we present a case of paroxysmal atrial fibrillation associated with NP specimen collection in a healthy healthcare provider undergoing COVID-19 testing during departmental screening. This response may have been caused by an exaggerated vagal tone triggered by the trigeminocardiac reflex. Less invasive collection methods, such as saliva testing, may be warranted in predisposed individuals.

Innovative and Integrated Contact Tracing: Indian Health Service, Arizona, December 2020-January 2021.

SARS-CoV-2 has exposed limitations of public health mitigation measures such as traditional case investigations and contact tracing. The Whiteriver Service Unit is a rural, acute care hospital on the Fort Apache Indian Reservation in Arizona with integrated health care delivery and public health services. During the first wave of COVID-19 cases in May-June 2020, we developed an innovative case investigation contact tracing approach that relied heavily on cross-trained personnel, in-person encounters, and baseline clinical evaluations. A second COVID-19 surge during December 13, 2020-January 31, 2021, caused incidence to peak at 413 cases per 100 000 community members. During that second surge, we investigated all 769 newly identified COVID-19 cases and notified 1911 (99.4%) of 1922 reported contacts. Median time interval from nasopharyngeal specimen collection to both case investigation and contact notification was 0 days (range, 0-5 days and 0-13 days, respectively). Our primary lesson was the importance of cross-trained personnel who integrated tasks along the testing-tracing continuum (eg, in-person interviews, prompt referral for additional testing and evaluation). These successive steps fed forward to identify new cases and their respective contacts. Our innovative community-based approach was both successful and efficient; our experience suggests that when adapted based on local needs, case investigation and contact tracing remain valuable and feasible public health tools, even in rural, resource-limited settings.

Performance and safety of the induced sputum procedure in young children in Malawi: a prospective study.

BackgroundCollecting sputum specimens is a challenge in infants and young children. We assessed the performance and safety of induced sputum (IS) collection in this population, embedded in a prospective study evaluating respiratory cryptosporidiosis in Malawian children with diarrheal disease.MethodsWe assessed the sputum quality and correlation with detection of Cryptosporidium spp. and evaluated safety and adverse events in 162 children.ResultsAmong 159 stool specimens tested, 34 (21%, 95% CI 15.0 to 28%) were positive for Cryptosporidium spp. There were 160 IS and 161 nasopharyngeal (NP) specimens collected. IS and NP specimen collection was performed for each patient. The majority of IS specimens (122/147; 83%) were clear in appearance and 132/147 (90%) were of good quality. Among the respiratory specimens tested, 10 (6.3%, 95% CI 2.5 to 10%) IS and 4 (3%, 95% CI 0 to 5%) NP were positive for Cryptosporidium spp. When stool cryptosporidium PCR was the gold standard, IS PCR sensitivity was higher (29%, 95% CI 22 to 37%) compared with NP PCR (12%, 95% CI 7 to 17%) for detection of Cryptosporidium spp. One (0.4%) adverse event occurred, consisting of a drop in oxygen saturations at the 30-min postprocedure evaluation. Consciousness level, median respiratory rate and oxygen saturations were unchanged, before or after IS.ConclusionsIS provides good quality specimens, is more sensitive than NP specimens for diagnosis of respiratory cryptosporidiosis, and collection can be performed safely in children hospitalized with diarrheal disease.

A systematic review of pregnant women with COVID-19 and their neonates.

BackgroundIn December 2019, a novel coronavirus disease (COVID-19) emerged in Wuhan, China, with an incredible contagion rate. However, the vertical transmission of COVID-19 is uncertain.ObjectivesThis is a systematic review of published studies concerning pregnant women with confirmed COVID-19 and their neonates.Search strategyWe carried out a systematic search in multiple databases, including PubMed, Web of Science, Google Scholar, Scopus, and WHO COVID-19 database using the following keywords: (Coronavirus) OR (novel coronavirus) OR (COVID-19) OR (COVID19) OR (COVID 19) OR (SARS-CoV2) OR (2019-nCoV)) and ((pregnancy) OR (pregnant) OR (vertical transmission) OR (neonate) OR (newborn) OR (placenta) OR (fetus) OR (Fetal)). The search took place in April 2020.Selection criteriaOriginal articles published in English were eligible if they included pregnant patients infected with COVID-19 and their newborns.Data collection and analysesThe outcomes of interest consisted of clinical manifestations of COVID-19 in pregnant patients with COVID-19 and also the effect of COVID-19 on neonatal and pregnancy outcomes.Main results37 articles involving 364 pregnant women with COVID-19 and 302 neonates were included. The vast majority of pregnant patients were in their third trimester of pregnancy, and only 45 cases were in the first or second trimester (12.4%). Most mothers described mild to moderate manifestations of COVID-19. Of 364 pregnant women, 25 were asymptomatic at the time of admission. The most common symptoms were fever (62.4%) and cough (45.3%). Two maternal deaths occurred. Some pregnant patients (12.1%) had a negative SARS‐CoV‐2 test but displayed clinical manifestations and abnormalities in computed tomography (CT) scan related to COVID‐19. Twenty‐two (6.0%) pregnant patients developed severe pneumonia. Two maternal deaths occurred from severe pneumonia and multiple organ dysfunction. Studies included a total of 302 neonates from mothers with COVID‐19. Of the studies that provided data on the timing of birth, there were 65 (23.6%) preterm neonates. One baby was born dead from a mother who also died from COVID-19. Of the babies born alive from mothers with COVID‐19, five newborns faced critical conditions, and two later died. A total of 219 neonates underwent nasopharyngeal specimen collection for SARS‐CoV‐2, of which 11 tested positive (5%). Seventeen studies examined samples of the placenta, breast milk, umbilical cord, and amniotic fluid, and all tested negative except one amniotic fluid sample.ConclusionsA systematic review of published studies confirm that the course of COVID-19 in pregnant women resembles that of other populations. However, there is not sufficient evidence to establish an idea that COVID-19 would not complicate pregnancy.

520. Longitudinal Analysis of SARS-CoV-2 Viruses in Hospitalized Adults

BackgroundThe rapid spread of SARS-CoV-2, the causative agent of Coronavirus disease 2019 (COVID-19), has been accompanied by the emergence of viral mutations, some of which may have distinct virological and clinical consequences. While whole genome sequencing efforts have worked to map this viral diversity at the population level, little is known about how SARS-CoV-2 may diversify within a host over time. This is particularly important for understanding the emergence of viral resistance to therapeutic interventions and immune pressure. The goal of this study was to assess the change in viral load and viral genome sequence within patients over time and determine if these changes correlate with clinical and/or demographic parameters.MethodsHospitalized patients admitted to Northwestern Memorial Hospital with a positive SARS-CoV-2 test were enrolled in a longitudinal study for the serial collection of nasopharyngeal specimens. Swabs were administered to patients by hospital staff every 4 ± 1 days for up to 32 days or until the patients were discharged. RNA was extracted from each specimen and viral loads were calculated by quantitative reverse transcriptase PCR (qRT-PCR). Specimens with qRT-PCR cycle threshold values less than or equal to 30 were subject to whole viral genome sequencing by reverse transcription, multiplex PCR, and deep sequencing. Variant populations sizes were estimated and subject to phylogenetic analysis relative to publicly available SARS-CoV-2 sequences. Sequence and viral load data were subsequently correlated to available demographic and clinical data.Results60 patients were enrolled from March 26th to June 20th, 2020. We observed an overall decrease in nasopharyngeal viral load over time across all patients. However, the temporal dynamics of viral load differed on a patient-by-patient basis. Several mutations were also observed to have emerged within patients over time.Distribution of SARS-CoV-2 viral loads in serially collected nasopharyngeal swabs in hospitalized adults as determined by qRT-PCR. Samples were collected every 4 ± 1 days (T#1–8) and viral load is displayed by log(copy number). ConclusionThese data indicate that SARS-CoV-2 viral loads in the nasopharynx decrease over time and that the virus can accumulate mutations during replication within individual patients. Future studies will examine if some of these mutations may provide fitness advantages in the presence of therapeutic and/or immune selective pressures.DisclosuresMichael G. Ison, MD MS, AlloVir (Consultant)

Probable causes and risk factors for positive SARS-CoV-2 test in recovered patients: Evidence from Brunei Darussalam.

Case reports of patients with coronavirus disease‐2019 (COVID‐19) who have been discharged and subsequently report positive reverse transcription‐polymerase chain reaction again (hereafter referred as “re‐positive”) do not fully describe the magnitude and significance of this issue. To determine the re‐positive rate (proportion) and review probable causes and outcomes, we conduct a retrospective study of all 119 discharged patients in Brunei Darussalam up till April 23. Patients who were discharged are required to self‐isolate at home for 14 days and undergo nasopharyngeal specimen collection postdischarge. Discharged patients found to be re‐positive were readmitted. We reviewed the clinical and epidemiological records of all discharged patients and apply log‐binomial models to obtain risk ratios for re‐positive status. One in five recovered patients subsequently test positive again for severe acute respiratory syndrome coronavirus 2—this risk is more than six times higher in persons aged 60 years and above. The average Ct value of re‐positive patients was lower predischarge compared with their readmission Ct value. Out of 111 close contacts tested, none were found to be positive as a result of exposure to a re‐positive patient. Our findings support prolonged but intermittent viral shedding as the probable cause for this phenomenon. We did not observe infectivity potential in these patients.

Suboptimal Biological Sampling as a Probable Cause of False-Negative COVID-19 Diagnostic Test Results.

False-negative severe acute respiratory syndrome coronavirus 2 test results can negatively impact the clinical and public health response to coronavirus disease 2019 (COVID-19). We used droplet digital polymerase chain reaction (ddPCR) to demonstrate that human DNA levels, a stable molecular marker of sampling quality, were significantly lower in samples from 40 confirmed or suspected COVID-19 cases that yielded negative diagnostic test results (ie, suspected false-negative test results) compared with a representative pool of 87 specimens submitted for COVID-19 testing. Our results support suboptimal biological sampling as a contributor to false-negative COVID-19 test results and underscore the importance of proper training and technique in the collection of nasopharyngeal specimens.

Safety management of nasopharyngeal specimen collection from suspected cases of coronavirus disease 2019

This article introduces safety management strategies of nasopharyngeal specimen collection from suspected cases of coronavirus disease 2019 in a tertiary designated hospital. The key points include establishing a special sampling room, strict sterilization of the entire environment, training of professional nurses, enhancement of personal protection, standardization of methods and processes for swab collection, and a timely and safety sample submission. More than 11,000 nasopharyngeal specimens were collected by eight nurses, with an average of 1,375 specimen swab collections each nurse, and no one was infected.

Surveillance of Respiratory Viruses in Long Term Care Facilities

ObjectiveTo assess the feasibility of conducting respiratory virus surveillance for residents of long term care facilities (LTCF) using simple nasal swab specimens and to describe the virology of acute respiratory infections (ARI) in LCTFs.IntroductionAlthough residents of LTCFs have high morbidity and mortality associated with ARIs, there is very limited information on the virology of ARI in LTCFs.[1,2] Moreover, most virological testing of LCTF residents is reactive and is triggered by a resident meeting selected surveillance criteria. We report on incidental findings from a prospective trial of introducing rapid influenza diagnostic testing (RIDT) in ten Wisconsin LTCFs over a two-year period with an approach of testing any resident with ARI.MethodsAny resident with new onset of respiratory symptoms consistent with ARI had a nasal swab specimen collected for RIDT by nursing staff. Following processing for RIDT (Quidel Sofia Influenza A+B FIA), the residual swab was placed into viral transport medium and forwarded to the Wisconsin State Laboratory of Hygiene and tested for influenza using RT-PCR (IVD CDC Human Influenza Virus Real-Time RT-PCR Diagnostic Panel), and for 17 viruses (Luminex NxTAG Respiratory Pathogen Panel [RPP]). The numbers of viruses in each of 7 categories [influenza A (FluA ), influenza B (FluB), coronaviruses (COR), human metapneumovirus (hMPV), parainfluenza (PARA), respiratory syncytial virus (RSV) and rhinovirus/enterovirus (R/E)], across the two years were compared using chi-square.ResultsTotals of 164 and 190 specimens were submitted during 2016-2017 and 2017-2018, respectively. RPP identified viruses in 56.2% of specimens, with no difference in capture rate between years (55.5% vs. 56.8%). Influenza A (21.5%), influenza B (16.5%), RSV (19.0%) and hMPV (16.5%) accounted for 73.5% of all detections, while coronaviruses (15.5%), rhino/enteroviruses (8.5%) and parainfluenza (2.5%) were less common. Specific distribution of viruses varied significantly across the two years (Table: X2=48.1, df=6; p&lt;0.001).ConclusionsSurveillance in LTCFs using nasal swabs collected for RIDT is highly feasible and yields virus identification rates similar to those obtained in clinical surveillance of ARI with collection of nasopharyngeal specimens by clinicians and those obtained in a school-based surveillance project of ARI with collection of combined nasal and oropharyngeal specimens collected by trained research assistants. Significant differences in virus composition occurred across the two study years. RSV varied little between years while hMPV demonstrated wide variation. Simple approaches to surveillance may provide a more comprehensive assessment of respiratory viruses in LTCF settings.References(1) Uršič T, Gorišek Miksić N, Lusa L, Strle F, Petrovec M. Viral respiratory infections in a nursing home: a six-month prospective study. BMC Infect Dis. 2016; 16: 637. Published online 2016 Nov 4. doi: 10.1186/s12879-016-1962-8(2) Masse S, Capai L, Falchi A. Epidemiology of Respiratory Pathogens among Elderly Nursing Home Residents with Acute Respiratory Infections in Corsica, France, 2013–2017. Biomed Res Int. 2017; 2017: 1423718. Published online 2017 Dec 17. doi: 10.1155/2017/1423718

Bordetella parapertussis outbreak in Southeastern Minnesota and the United States, 2014.

Whooping cough is traditionally ascribed to Bordetella pertussis; however, Bordetella parapertussis can cause a similar clinical syndrome. This study describes an outbreak of B. parapertussis in Southeastern Minnesota and the United States (US) in 2014. This was a retrospective analysis of Mayo Clinic and Mayo Medical Laboratories patients who tested positive for B. parapertussis from 2012 to 2014. The medical records of Mayo Clinic patients who tested positive in 2014 were reviewed for demographic information, presenting symptoms, disease course, and vaccination history. In Southeast Minnesota, 81% of the 31 patients who tested positive for B. parapertussis in 2014 were found to be positive from October through December. Their mean age was 5.9 years. Five reported “exposure to pertussis.” Two pairs of siblings were affected. Patients reported having had symptoms for an average of 2.6 weeks before nasopharyngeal specimen collection for B. parapertussis testing. Cough was the primary symptom reported. Forty percent reported posttussive vomiting, 40% coryza, 32% apnea/sleep disturbance, and 12% sore throat. All were current with pertussis vaccination. Based on the review of national data, an outbreak occurred nationally in the Northeast and Midwest US over the same time period. In 2014, there was an outbreak of B. parapertussis in Southeastern Minnesota and likely other parts of the US. The presenting illness was similar to that of B. pertussis. All patients were vaccinated against pertussis, suggesting that pertussis vaccination is ineffective against B. parapertussis.

Epidemiologic, clinical, and virologic characteristics of human rhinovirus infection among otherwise healthy children and adults: Rhinovirus among adults and children

Backgroundhuman rhinovirus (HRV) is a major cause of influenza-like illness (ILI) in adults and children. Differences in disease severity by HRV species have been described among hospitalized patients with underlying illness. Less is known about the clinical and virologic characteristics of HRV infection among otherwise healthy populations, particularly adults. Objectivesto characterize molecular epidemiology of HRV and association between HRV species and clinical presentation and viral shedding. Study designobservational, prospective, facility-based study of ILI was conducted from February 2010 to April 2012. Collection of nasopharyngeal specimens, patient symptoms, and clinical information occurred on days 0, 3, 7, and 28. Patients recorded symptom severity daily for the first 7 days of illness in a symptom diary. HRV was identified by RT-PCR and genotyped for species determination. Cases who were co-infected with other viral respiratory pathogens were excluded from the analysis. We evaluated the associations between HRV species, clinical severity, and patterns of viral shedding. Resultseighty-four HRV cases were identified and their isolates genotyped. Of these, 62 (74%) were >18 years. Fifty-four were HRV-A, 11HRV-B, and 19HRV-C. HRV-C infection was more common among children than adults (59% vs. 10%, P<0.001). Among adults, HRV-A was associated with higher severity of upper respiratory symptoms compared to HRV-B (P=0.02), but no such association was found in children. In addition, adults shed HRV-A significantly longer than HRV-C (P trend=0.01). Conclusionsamong otherwise healthy adults with HRV infection, we observed species-specific differences in respiratory symptom severity and duration of viral shedding.

Comparative Evaluation of a Rapid Influenza Diagnostic Test in the Pediatric Emergency Department Setting Using Three Specimen Collection Methods

Background: Rapid, accurate, point-of-care detection of influenza virus infection is desirable for the outpatient management of children. Several collection methods including nasopharyngeal wash (NPW), nasopharyngeal swab (NPS) and nasal swab (NS) are available for testing by commercially available rapid influenza diagnostic tests. Unfortunately, the collection of nasopharyngeal specimens by NPW is uncomfortable and time-consuming. Swabs of the nose and pharynx are better tolerated by patients and easier to collect. To date, however, no studies have compared the yield from swabs (NPS and NS) to that from NPW for diagnosing influenza in children. Study Objective: To compare the diagnostic yield of a rapid antigen detection test for influenza in samples obtained by three different specimen collection methods.