Nasal Specimens Research Articles

COVID-19 mass testing and sequencing: Experiences from a laboratory in Western Kenya.

BackgroundThe Basic Science Laboratory (BSL) of the Kenya Medical Research Institute/Walter Reed Project in Kisumu, Kenya addressed mass testing challenges posed by the emergent coronavirus disease 2019 (COVID-19) in an environment of global supply shortages. Before COVID-19, the BSL had adequate resources for disease surveillance and was therefore designated as one of the testing centres for COVID-19.InterventionBy April 2020, the BSL had developed stringent safety procedures for receiving and mass testing potentially infectious nasal specimens. To accommodate increased demand, BSL personnel worked in units: nucleic acid extraction, polymerase chain reaction, and data and quality assurance checks. The BSL adopted procedures for tracking sample integrity and minimising cross-contamination.Lessons learntBetween May 2020 and January 2022, the BSL tested 63 542 samples, of which 5375 (8.59%) were positive for COVID-19; 1034 genomes were generated by whole genome sequencing and deposited in the Global Initiative on Sharing All Influenza Data database to aid global tracking of viral lineages. At the height of the pandemic (August and November 2020, April and August 2021 and January 2022), the BSL was testing more than 500 samples daily, compared to 150 per month prior to COVID-19. An important lesson from the COVID-19 pandemic was the discovery of untapped resilience within BSL personnel that allowed adaptability when the situation demanded. Strict safety procedures and quality management that are often difficult to maintain became routine.RecommendationsA fundamental lesson to embrace is that there is no ‘one-size-fits-all’ approach and adaptability is the key to success.

Magnitude and Determinants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Household Transmission: A Longitudinal Cohort Study.

BackgroundHouseholds have emerged as important venues for SARS-CoV-2 transmission. Little is known, however, regarding the magnitude and determinants of household transmission in increasingly vaccinated populations.MethodsFrom September 2020 to January 2022, symptomatic non-hospitalized individuals with SARS-CoV-2 infection by RNA detection were identified within 5 days of symptom onset; all individuals resided with at least one other SARS-CoV-2-uninfected household member. These infected persons (cases) and their household members (contacts) were subsequently followed with questionnaire-based measurement and serial nasal specimen collection. The primary outcome was SARS-CoV-2 infection among contacts.ResultsWe evaluated 42 cases and their 74 household contacts. Among the contacts, 32 (43%) became infected, of whom 5/32 (16%) were asymptomatic; 81% of transmissions occurred by 5 days after the case’s symptom onset. From 21 unvaccinated cases, 14-day cumulative incidence of SARS-CoV-2 infection among contacts was 18/40 (45%; 95% CI: 29, 62), most of whom were unvaccinated. From 21 vaccinated cases, 14-day cumulative incidence of SARS-CoV-2 infection was 14/34 (41%; 95% CI: 25, 59) among all contacts and 12/29 (41%; 95% CI: 24, 61) among vaccinated contacts. At least one co-morbid condition among cases and 10 or more days of RNA detection in cases were associated with increased risk of infection among contacts.ConclusionsAmong households including individuals with symptomatic SARS-CoV-2 infection, both vaccinated-to-vaccinated and unvaccinated-to-unvaccinated transmission of SARS-CoV-2 to household contacts was common. Because vaccination alone did not notably reduce risk of infection, household contacts will need to employ additional interventions to avoid infection.

The high frequency of mecA and Als3p genes among Staphylococcus aureus and Candida species isolated from patients with malignancies on chemotherapy

The present study aimed to survey the prevalence of methicillin-resistant Staphylococcus aureus and Candida species oral and nasal co-colonization among patients with malignancies on chemotherapy in Tehran, Iran. In a cross-sectional single-center study performed from October until the end of December 2020, oral and nasal specimens were collected using dry sponge swabs from patients with different malignancies under chemotherapy in Masih Daneshvari Hospital, Tehran, Iran. We used the disk diffusion method to the screening of oxacillin (methicillin) resistance among S. aureus isolates. The final identification of MRSA strains and the frequency of hyphal adhesin Als3p was performed using the PCR method with a specific primer that targeted mecA and Als3p genes, respectively. A total of 170 oral and nasal specimens were collected from 170 adult patients. Oral colonization by S. aureus, MRSA, and Candida species was found in 20 (11.8%), 11 (6.5%), and 68 (40%) patients, respectively, while nasal colonization by S. aureus and MRSA and Candida species was found in 26 (15.3%), 17 (10%) and 7 (4.1%) patients, respectively. The total colonization of MRSA and Candida spp. in both oral and nasal was 14.7% (n = 25/170) and 41.2% (n = 70/170), respectively. All MRSA isolates and Candida species were positive for mecA and Als3p genes, respectively. The present study revealed the importance of polymicrobial infection among patients with different malignancies and presumed that S. aureus can use Candida adhesion Als3p to create systemic infections in immunocompromised patients.

Diagnostic Accuracy of CHROMagar MRSA for Detection of Methicillin-Resistant Staphylococcus Aureus (MRSA) from Screening Swab Specimens

Objective: To determine the diagnostic accuracy of CHROMagar MRSA for detecting MRSA from screening swab specimens keeping the Cefoxitin disk diffusion test as the reference method.
 Study Design: A cross-sectional validation study.
 Place and duration of study: Department of Microbiology, Armed Forces Institute of Pathology (AFIP), Rawalpindi Pakistan, from Mar to Aug 2019.
 Methodology: A total of 243 screening swab specimens, e.g., axillary, nasal and web swabs, each of hospitalized patients and healthcare workers (HCW) submitted for MRSA screening were included in the study and were processed simultaneously on blood agar, MacConkey agar and CHROMagar MRSA. The agar plates were incubated at 35°C ± 2°C for 18-24 hours in ambient air. The cefoxitin disk diffusion test followed the isolation and identification of MRSA according to the latest Clinical and Laboratory Standards Institute (CLSI) guidelines. In CHROMagar MRSA screening, after incubation, plates were examined for the presence of mauve colonies (MRSA detected), and the results were obtained and validated against the reference method of Cefoxitin disk diffusion.
 Results: Overall, the diagnostic accuracy of CHROMagar MRSA for detecting MRSA was 97.53%. Diagnostic accuracy of CHROMagar MRSA was 95.1%, 97.5% and 100% in axillary, nasal and web specimens, respectively. The rate of MRSA detection was maximum in axillary swabs, i.e., 40.7%, followed by 29.6% and 9.8% in nasal and web swabs, respectively.
 Conclusion: CHROMagar MRSA is found to be accurate for the detection of MRSA. It is reliable, easy to perform, less timeconsuming, and cost-effective. It is an affordable alternative to the conventional..............

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Codetection With Influenza A and Other Respiratory Viruses Among School-Aged Children and Their Household Members-12 March 2020 to 22 February 2022, Dane County, Wisconsin.

BackgroundConcurrent detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and another respiratory virus in individuals can document contemporaneous circulation. We used an ongoing, community-based study of school-aged children and their households to evaluate SARS-CoV-2 co-detections with other respiratory viruses in a non-medically attended population over a two-year period.MethodsHousehold enrollment was predicated on an acute respiratory illness in a child residing in that household who was also a kindergarten through 12th grade student in the participating school district. Demographic, symptom and household composition data, and self-collected nasal specimens were obtained on the recruitment day, and 7 and 14 days later, from the index child and all other household members. All specimens were tested for SARS-CoV-2/influenza A/B by RT-PCR. Day 0 specimens from the index children were simultaneously tested for 17 viruses using a commercial respiratory pathogen panel (RPP). To assess viral co-detections involving SARS-CoV-2, all household specimens were tested via RPP if the index child’s Day 0 specimen tested positive to any of the 17 viral targets in RPP and any household member tested positive for SARS-CoV-2.ResultsOf 2,109 participants (497 index children in 497 households with 1,612 additional household members), two (0.1%) were positive for both SARS-CoV-2 and influenza A; an additional 11 (0.5%) were positive for SARS-CoV-2 and another RPP-covered respiratory virus. Co-detections predominantly affected school-aged children (12 out of 13 total) and were noted in 11 of 497 households.ConclusionsSARS-CoV-2 co-detections with other respiratory viruses were uncommon and predominated in school-aged children.

#66 Clinical characteristics and outcomes of children with single or co-detected rhinovirus-associated acute respiratory infection in Middle Tennessee

Abstract Background Rhinovirus (RV) is one of the most common viral etiologies of acute respiratory infection (ARI)—the leading infectious cause of mortality in young children. Multiple respiratory viruses may be detected with RV in children with ARI, but the clinical significance of viral co-detection is unclear. We aimed to compare the clinical characteristics and outcomes of children with ARI associated with RV-only detection or RV co-detection. Method We conducted a prospective viral surveillance study (11/2015–7/2016) in Nashville, Tennessee. Children <18 years old who presented to the emergency department (ED) or were hospitalized with fever and/or respiratory symptoms of <14 days duration were eligible if they resided in one of nine selected counties in Middle Tennessee. Demographics and clinical characteristics were collected by parental interviews and medical chart abstractions. Nasal and/or throat specimens were collected and tested for RV, RSV, metapneumovirus, adenovirus, parainfluenza 1–4, and influenza A–C using real-time reverse transcriptase polymerase chain reaction assays. We compared clinical characteristics and outcomes of children with RV-only detection or RV co-detection using Pearson's χ2 test for categorical variables and linear regression with robust standard errors for continuous variables. Results Of 1,250 children who were enrolled, 904 (72.3%) were positive for at least one virus. RV was detected in 406 virus-positive children (44.9%), of whom 117 (28.8%) had RV co-detection. The most common RV co-detection pair was RV/RSV (n=36). The mean age of children with RV co-detection was lower than those with RV-only detection (2.6 ± 2.7 years vs. 4.3 ± 4.4 years; p<0.001). The signs and symptoms of children with RV-only detection and those with RV co-detection are compared in Table 1. A total of 283 children with RV were discharged from the ED (69.7%), of whom 89 (31.4%) had RV co-detection. Children with RV co-detection who were discharged from the ED were less likely to have a diagnosis of asthma/reactive airway disease (RAD) than those with RV-only detection (10.1% vs. 21.6%; p=0.019) but more likely to be diagnosed with bronchiolitis (18.0% vs. 1.5%; p<0.001). Of the 123 hospitalized children with RV, 28 (22.8%) had RV co-detection. Hospitalized children with RV co-detection were less likely to have an admission diagnosis of asthma/RAD than those with RV-only detection (7.1% vs. 43.2%; p<0.001) but more likely to be diagnosed with bronchiolitis (32.1% vs. 14.7%; p=0.038) and pneumonia (32.1% vs. 8.4%; p<0.001). We did not identify differences in hospitalization, intensive care unit admission, supplemental oxygen use, or length of stay between children with RV-only detection and RV co-detection. Conclusion We did not find evidence that RV co-detection was associated with worse outcomes in children with ARI. However, the clinical presentation of children with RV co-detection differs from that of children with RV-only detection. These distinctions warrant consideration in the diagnostic evaluation and management of RV-positive children. Further studies are needed to describe the distinct clinical presentations of RV/non-RV pairs and RV species.

Evaluation of the Panbio COVID-19 Antigen Rapid Diagnostic Test in Subjects Infected with Omicron Using Different Specimens.

ABSTRACTCommunity testing is a crucial tool for the early identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and transmission control. The emergence of the highly mutated Omicron variant (B.1.1.529) raised concerns about its primary site of replication, impacting sample collection and its detectability by rapid antigen tests. We tested the performance of the Panbio antigen rapid diagnostic test (Ag-RDT) using nasal and oral specimens for COVID-19 diagnosis in 192 symptomatic individuals, with quantitative reverse transcription-PCR (RT-qPCR) of nasopharyngeal samples as a control. Variant of concern (VOC) investigation was performed with the 4Plex SARS-CoV-2 screening kit. The SARS-CoV-2 positivity rate was 66.2%, with 99% of the positive samples showing an amplification profile consistent with that of the Omicron variant. Nasal Ag-RDT showed higher sensitivity (89%) than oral (12.6%) Ag-RDT. Our data showed good performance of the Ag-RDT in a pandemic scenario dominated by the Omicron VOC. Furthermore, our data also demonstrated that the Panbio COVID-19 antigen rapid diagnostic test does not provide good sensitivity with oral swabs for Omicron Ag-RDT detection.IMPORTANCE This study showed that the antigen rapid test for COVID19 worked fine using nasal swabs when it was utilized in patients infected with the Omicron variant, showing a concordance with PCR in 93% of patients tested. The nasal swab yielded more reliable results than the oral swab when an antigen rapid diagnosis test (the Panbio COVID-19 antigen rapid diagnostic test) was used in patients infected with the Omicron variant.

Establishment of a patient-derived organoid model and living biobank for nasopharyngeal carcinoma

Background Recurrent nasopharyngeal carcinoma (NPC) remains a major challenge for clinicians and scientists. Tumor organoid is a revelational disease model that highly resembled the heterogeneity and histopathological characteristics of original tumors. This study aimed to optimize the modeling process of patient-derived NPC organoids (NPCOs), and establish a living-biobank of NPCs to study the mechanism and explore the more effective treatment of the disease.MethodsSixty-two fresh NPC tissue samples and 15 normal mucosa samples were collected for 3-dimensional (3D) organoid culture. The organoids were confirmed using hematoxylin and eosin assays. The expression levels of CD133, CD44, BMI-1, and Epstein-Barr virus (EBV)-encoded small RNAs (EBERs) were detected by immunohistochemistry (IHC) and in situ hybridization (ISH). Recurrent NPCOs were frozen in liquid nitrogen for 6 months and then resuscitated and passaged.ResultsWe identified a novel two-step enzymatic strategy for the treatment of NPC and nasal mucosa specimens and an optimal medium for culturing NPCOs and nasal mucosa organoids (NMOs). Organoid cultures were generated from 34 primary NPC samples, 28 recurrent NPC samples, and 15 normal mucosa samples. The success rates for primary NPCO, recurrent NPCO, and NMO formation were 47.06%, 81.25%, and 86.5%, respectively. All the NPCOs were EBER positive and CK7 negative. Recurrent NPCOs had higher expressions of stem cell markers, including BMI-1, CD44, and CD133. Additionally, recurrent NPCOs could be cultured to passage 4 and frozen and revived repeatedly, while primary NPCOs were challenging to culture.Conclusions In summary, we successfully established a living biobank using the NPCO model, which has enormous potential in basic and clinical research on NPC.

Performance evaluation of STANDARD Q COVID-19 Ag home test for the diagnosis of COVID-19 during early symptom onset.

BackgroundSurveillance and control of SARS‐CoV‐2 outbreak through gold standard detection, that is, real‐time polymerase chain reaction (RT‐PCR), become a great obstacle, especially in overwhelming outbreaks. In this study, we aimed to analyze the performance of rapid antigen home test (RAHT) as an alternative detection method compared with RT‐PCR.MethodsIn total, 79 COVID‐19‐positive and 217 COVID‐19‐negative patients confirmed by RT‐PCR were enrolled in this study. A duration from symptom onset to COVID‐19 confirmation of <5 days was considered a recruiting criterion for COVID‐19‐positive cases. A nasal cavity specimen was collected for the RAHT, and a nasopharyngeal swab specimen was collected for RT‐PCR.ResultsSensitivity of the STANDARD Q COVID‐19 Ag Home Test (SD Biosensor, Korea), compared with RT‐PCR, was 94.94% (75/79) (95% [confidence interval] CI, 87.54%–98.60%), and specificity was 100%. Sensitivity was significantly higher in symptomatic patients (98.00%) than in asymptomatic (89.66%) patients (p‐value = 0.03). There was no difference in sensitivity according to the duration of symptom onset to confirmation (100% for 0–2 days and 96.97% for 3–5 days, respectively) (p‐value = 1.00). The RAHT detected all 51 COVID‐19 patients whose Ct values were ≤25 (100%), whereas sensitivity was 73.33% (11/15) among patients with Ct values >25 (p‐value = 0.01).ConclusionThe RAHT showed an excellent sensitivity for COVID‐19‐confirmed cases, especially for those with symptoms. There was a decrease in sensitivity when the Ct value is over 25, indicating that RAHT screening may be useful during the early phase of symptom onset, when the viral numbers are higher and it is more transmissible.

Time to speed up the diagnostic evaluation in clinically suspected rhinosinusitis patients: A debate on the conventional versus molecular workup to establish fungal infective etiology for prompt management.

Rhinosinusitis (RS) is a clinical and radiological diagnosis that rarely reaches a proper infective etiological diagnosis. The most dreaded fact about invasive fungal rhinosinusitis is its poor prognosis in immunocompromised patients with a 60-80% mortality rate. The present study highlights and compares the various diagnostic techniques to establish a fungal etiological diagnosis in clinically suspected cases of RS from nasal biopsy specimens, with the emphasis on the molecular diagnostic approach. This prospective study included a total of 34 clinically suspected cases of RS who had recently undergone functional endoscopic sinus surgery (FESS)/biopsy from nasal polyps. Various laboratory methods (microbiological and histopathological) were utilized, including direct microscopic examination of clinical samples and fungal culture isolation. The molecular detection method of polymerase chain reaction (PCR) from clinical samples was also explored simultaneously. Serum immunoglobulin-E (IgE) testing of patients was also performed. Out of 34 clinically suspected RS cases, fungal etiology was established in a total of 18 cases, 17 of whom were culture-proven. A total of 15 and 14 culture-proven cases were also detected on direct microscopic examination by potassium hydroxide (KOH) mount and histopathological staining, respectively. One case was additionally identified by molecular method. Aspergillus flavus complex was the most common pathogen isolated in culture. Allergic fungal RS was the most common type, followed by acute and chronic invasive types among all fungal RS cases. Accurate and prompt etiological diagnosis of fungal RS is still lagging with fewer options for quick results. Although microscopy and culture isolation can't be replaced, PCR is a sensitive and specific method that should be incorporated as a supplementary tool for the early diagnosis and management, considering the delayed growth of fungi.

Effect of Thymoquinone and Transforming Growth Factor-β1 on the Cell Viability of Nasal Polyp-Derived Fibroblast

BACKGROUND: Nasal polyps are benign masses in the nasal cavity and the abnormal growth of sinonasal tissue due to a chronic inflammatory process. Many fibroblasts populate the nasal polyp stroma release cytokines such as Transforming Growth Factor (TGF) and producing a variety of cytokines resulting in inflammatory cell infiltration. Thymoquinone (TQ) is the main active component in Nigella sativa oil and has the ability to reduces cell viability in many cancer cell line. AIM: The purpose of this study was to determine the effect of TQ and TGF-β1 on cell viability of Nasal Polyp-Derived Fibroblast. MATERIALS AND METHODS: Nasal polyp-derived fibroblasts were isolated from nasal polyp specimen and treated with various concentrations of TQ at 1–1000 μM and TGF-β1 at 5 ng/ml to determine the cell viability using the Cell Counting Kit-8 assay after 48 h incubation. RESULTS: TQ significantly reduced the viability of nasal polyp fibroblast cells to 72.49% at 20 μM and reduced to 5% at 50 μM until 1000 μM with IC50 at 21.93 μM. TGF-β1 at 5 ng/ml significantly reduced the viability of nasal polyp fibroblast cells to 81.96% and TGF-β1 appears to have a dual effect that depends on the concentration of TQ. CONCLUSION: This study proved that TQ and TGF-β1 were able to reduce the viability of nasal polyp fibroblast cells.

110 Clinical Presentations of Adult and Pediatric SARS-CoV-2-Positive Cases in a Community Cohort

OBJECTIVES/GOALS: The spectrum of disease caused by SARS-CoV-2 ranges from asymptomatic detection to severe illness, with varying presentations by age. Therefore, we aimed to compare the clinical characteristics between children and adults with SARS-CoV-2. METHODS/STUDY POPULATION: From March 20, 2020, to August 18, 2021, we conducted SARS-CoV-2 surveillance in individuals from metropolitan Nashville, TN. Children with multisystem inflammatory syndrome were excluded. Analyses were restricted to individuals with SARS-CoV-2 infection confirmed by detection of viral RNA in nasal specimens using reverse-transcription quantitative polymerase chain reaction (RT-qPCR) and/or by detection of serum IgG to the SARS-CoV-2 spike and nucleocapsid proteins using enzyme-linked immunosorbent assay (ELISA). Those with negative RT-qPCR results, but a positive ELISA within 4-6 weeks of symptom onset, were classified as SARS-CoV-2 positive. Clinical characteristics between children and adults were compared with Pearson’s chi square. Illness duration was compared using Kaplan Meier estimators. RESULTS/ANTICIPATED RESULTS: Overall, 426/826 (49%) individuals (children: 57 [13%); adults: 369 [87%]) were SARS-CoV-2 positive, with median ages of 12 and 41 years, respectively. Most individuals were female (54%) and white, non-Hispanic (79%). Compared to adults, children were more likely to be asymptomatic (children: 16% vs. adults: 5%; p=0.001). In contrast, symptomatic adults were more likely to report cough (71% vs. 56%), wheezing (21% vs. 8%), shortness of breath (45% vs. 19%), ageusia (67% vs. 23%), and anosmia (64% vs 27%) than symptomatic children (p&lt;0.05). Mean illness duration was shorter in children than adults: 7 days (95% CI: 5.1, 8.9) vs. 14 days (95% CI: 12.4,15.0), respectively. A total of 5% (18/352) of adults reported symptoms lasting ? 4 weeks (range: 31-96 days), whereas all symptoms in children resolved by 31 days. DISCUSSION/SIGNIFICANCE: Overall, children with SARS-CoV-2 present with a shorter and milder disease course compared to adults. Further studies are needed to understand SARS-CoV-2 illness severity across the lifespan.

Participants' experience in using a point of Care Rapid Antigen Test (RAT) for SARS-CoV-2.

Learning objectives: On completion of this presentation, participant should be able to: Understand the feasibility of RAT for SARS-CoV-2 screening in primary care Understand the role of RAT for SARS-CoV-2 screening in prevention of COVID-19 transmission in community Context: The COVID-19 pandemic has paralyzed human interactions worldwide. At least half of COVID-19 transmissions could originate from asymptomatic individuals. Rapid Antigen Testing (RAT) with nasal sampling at the point of care is inexpensive, fast and less invasive than PCR testing. Objective: The overall study objective was to examine the feasibility of point-of-care RAT for detecting SARS-CoV-2 amongst an asymptomatic population living in congregate housing. Design: Cross-sectional survey. Setting: This study was conducted at the University of British Columbia (UBC). Approximately 1500 undergraduate student were at the study site during February-April 2021. Population: Students living in UBC housing and staff working in the UBC housing sites were eligible. People testing positive for COVID-19 in the prior 90 days were excluded from the study. Intervention: The BD Veritor testing kit was used to test bilateral nasal specimens. Results were ready by the small BD Veritor reader. Outcome measures: Experiences of surveyed participants completing RAT. The survey was conducted during the last three weeks the site was open. Results: A total of 223 participants consisting of 134 (60%) females and 89 (40%) males completed the survey for a 37% response rate. Participants were mainly of European descent (45%), though there were East Asians (18%), African/ Caribbean (5%) and Indigenous (3%) people who also completed the survey. Almost all (98%) reported that RAT was acceptable/very acceptable and 97% would take another test. Participants believed they would test negative given their careful observation of public health measures such as hand washing, mask wearing and restricting contacts to their small "bubble". Their expectation of testing negative was based on having no or minimal interactions with any person who had tested positive. More than two thirds of participants reported RAT provide them peace of mind and reduced anxiety levels. Participants found the RAT to be safe, easy, accessible and rapid. Conclusions: Rapid antigen testing for detecting COVID-19 is well accepted and could support the detection of infection at an early stage amongst asymptomatic individuals while easing their worries.

IRIS: Infection with RespIratory Syncytial Virus in infants—a prospective observational cohort study

BackgroundRespiratory syncytial virus (RSV) is the most common cause of acute lower respiratory tract infection in infants. Globally, RSV is responsible for approximately 3.2 million hospital admissions and about 60,000 in-hospital deaths per year.MethodsInfection with RespIratory Syncytial Virus (IRIS) is an observational, multi-centre study enrolling infants with severe RSV infection and healthy controls. Inclusion criteria are age between 0 and 36 months and hospitalisation due to RSV infection at three German sites. Exclusion criteria are premature birth, congenital or acquired bronchopulmonary or cardiac diseases, and immunodeficiency. Healthy control probands are enrolled via recruitment of patients undergoing routine surgical procedures. Blood and respiratory specimens are collected upon admission, and RSV and other pathogens are analysed by multiplex polymerase chain reaction. Different biomaterials, including plasma, nasal lining fluid, blood cells, DNA, and RNA specimens, are sampled in a dedicated biobank. Detailed information on demographic characteristics and medical history is recorded, and comprehensive clinical data, including vital signs, medication, and interventions.DiscussionThe IRIS study aims to discover host and viral factors controlling RSV disease courses in infants. The approach including multi-omics characterisation in clinically well-characterized children with RSV bronchiolitis seeks to improve our understanding of the immune response against this virus. It may disclose novel diagnostic and treatment approaches for respiratory infections in infants.Trial registration: ClinicalTrials.gov, NCT04925310. Registered 01 October 2021—Retrospectively registered. https://clinicaltrials.gov/ct2/show/NCT04925310?cond=NCT04925310&draw=2&rank=1

Evaluation of the Diagnostic Accuracy of Nasal Cavity and Nasopharyngeal Swab Specimens for SARS-CoV-2 Detection via Rapid Antigen Test According to Specimen Collection Timing and Viral Load.

The rapid diagnosis of SARS-CoV-2 is an essential aspect in the detection and control of the spread of COVID-19. We evaluated the accuracy of the rapid antigen test (RAT) using samples from the nasal cavity and nasopharynx based on sample collection timing and viral load. We enrolled 175 patients, of which 71 patients and 104 patients had tested positive and negative, respectively, based on real time-PCR. Nasal cavity and nasopharyngeal swab samples were tested using STANDARD Q COVID-19 Ag tests (Q Ag, SD Biosensor, Korea). The sensitivity of the Q Ag test was 77.5% (95% confidence interval [CI], 67.8–87.2%) for the nasal cavity and 81.7% (95% [CI, 72.7–90.7%) for the nasopharyngeal specimens. The RAT results showed a substantial agreement between the nasal cavity and nasopharyngeal specimens (Cohen’s kappa index = 0.78). The sensitivity of the RAT for nasal cavity specimens exceeded 89% for <5 days after symptom onset (DSO) and 86% for Ct of E and RdRp < 25. The Q Ag test performed fairly well, especially in the early DSO when a high viral load was present, and the nasal cavity swab can be considered an alternative site for the rapid diagnosis of COVID-19.

SARS-CoV-2 incidence, transmission, and reinfection in a rural and an urban setting: results of the PHIRST-C cohort study, South Africa, 2020–21

SummaryBackgroundBy August, 2021, South Africa had been affected by three waves of SARS-CoV-2; the second associated with the beta variant and the third with the delta variant. Data on SARS-CoV-2 burden, transmission, and asymptomatic infections from Africa are scarce. We aimed to evaluate SARS-CoV-2 burden and transmission in one rural and one urban community in South Africa.MethodsWe conducted a prospective cohort study of households in Agincourt, Mpumalanga province (rural site) and Klerksdorp, North West province (urban site) from July, 2020 to August, 2021. We randomly selected households for the rural site from a health and sociodemographic surveillance system and for the urban site using GPS coordinates. Households with more than two members and where at least 75% of members consented to participate were eligible. Midturbinate nasal swabs were collected twice a week from household members irrespective of symptoms and tested for SARS-CoV-2 using real-time RT-PCR (RT-rtPCR). Serum was collected every 2 months and tested for anti-SARS-CoV-2 antibodies. Main outcomes were the cumulative incidence of SARS-CoV-2 infection, frequency of reinfection, symptomatic fraction (percent of infected individuals with ≥1 symptom), the duration of viral RNA shedding (number of days of SARS-CoV-2 RT-rtPCR positivity), and the household cumulative infection risk (HCIR; number of infected household contacts divided by the number of susceptible household members).Findings222 households (114 at the rural site and 108 at the urban site), and 1200 household members (643 at the rural site and 557 at the urban site) were included in the analysis. For 115 759 nasal specimens from 1200 household members (follow-up 92·5%), 1976 (1·7%) were SARS-CoV-2-positive on RT-rtPCR. By RT-rtPCR and serology combined, 749 of 1200 individuals (62·4% [95% CI 58·1–66·4]) had at least one SARS-CoV-2 infection episode, and 87 of 749 (11·6% [9·4–14·2]) were reinfected. The mean infection episode duration was 11·6 days (SD 9·0; range 4–137). Of 662 RT-rtPCR-confirmed episodes (>14 days after the start of follow-up) with available data, 97 (14·7% [11·9–17·9]) were symptomatic with at least one symptom (in individuals aged <19 years, 28 [7·5%] of 373 episodes symptomatic; in individuals aged ≥19 years, 69 [23·9%] of 289 episodes symptomatic). Among 222 households, 200 (90·1% [85·3–93·7]) had at least one SARS-CoV-2-positive individual on RT-rtPCR or serology. HCIR overall was 23·9% (195 of 817 susceptible household members infected [95% CI 19·8–28·4]). HCIR was 23·3% (20 of 86) for symptomatic index cases and 23·9% (175 of 731) for asymptomatic index cases (univariate odds ratio [OR] 1·0 [95% CI 0·5–2·0]). On multivariable analysis, accounting for age and sex, low minimum cycle threshold value (≤30 vs >30) of the index case (OR 5·3 [2·3–12·4]) and beta and delta variant infection (vs Wuhan-Hu-1, OR 3·3 [1·4–8·2] and 10·4 [4·1–26·7], respectively) were associated with increased HCIR. People living with HIV who were not virally supressed (≥400 viral load copies per mL) were more likely to develop symptomatic illness when infected with SAR-CoV-2 (OR 3·3 [1·3–8·4]), and shed SARS-CoV-2 for longer (hazard ratio 0·4 [95% CI 0·3–0·6]) compared with HIV-uninfected individuals.InterpretationIn this study, 565 (85·3%) SARS-CoV-2 infections were asymptomatic and index case symptom status did not affect HCIR, suggesting a limited role for control measures targeting symptomatic individuals. Increased household transmission of beta and delta variants was likely to have contributed to successive waves of SARS-CoV-2 infection, with more than 60% of individuals infected by the end of follow-up.FundingUS CDC, South Africa National Institute for Communicable Diseases, and Wellcome Trust.

Development and Large-Scale Testing of a Novel One-Step Triplex RT-qPCR Assay for Simultaneous Detection of "Neurotropic" Porcine Sapeloviruses, Teschoviruses (Picornaviridae) and Type 3 Porcine Astroviruses (Astroviridae) in Various Samples including Nasal Swabs.

Porcine sapeloviruses, teschoviruses of family Picornaviridae and type 3 porcine astroviruses of family Astroviridae are (re-)emerging enteric pathogens that could be associated with severe, disseminated infections in swine, affecting multiple organs including the central nervous system (CNS). Furthermore, small-scale pioneer studies indicate the presence of these viruses in porcine nasal samples to various extents. The laboratory diagnostics are predominantly based on the detection of the viral RNA from faecal and tissue samples using different nucleic-acid-based techniques such as RT-qPCR. In this study, a novel highly sensitive one-step triplex RT-qPCR assay was introduced which can detect all known types of neurotropic sapelo-, tescho- and type 3 astroviruses in multiple types of samples of swine. The assay was evaluated using in vitro synthesized RNA standards and a total of 142 archived RNA samples including known sapelo-, tescho- and type 3 astrovirus positive and negative CNS, enteric and nasal specimens. The results of a large-scale epidemiological investigation of these viruses on n = 473 nasal swab samples from n = 28 industrial-type swine farms in Hungary indicate that all three neurotropic viruses, especially type 3 astroviruses, are widespread and endemically present on most of the investigated farms.

Multi-body-site colonization screening cultures for predicting multi-drug resistant Gram-negative and Gram-positive bacteremia in hematological patients

BackgroundTo investigate the multi-drug resistant bacteria (MDRB) colonization rate in hematological patients hospitalized for any cause using a multi-body-site surveillance approach, and determine the extent to which this screening strategy helped anticipate MDRB bloodstream infections (BSI).MethodsSingle-center retrospective observational study including 361 admissions documented in 250 adult patients. Surveillance cultures of nasal, pharyngeal, axillary and rectal specimens (the latter two combined) were performed at admission and subsequently on a weekly basis. Blood culture samples were incubated in an automated continuous monitoring blood culturing instrument (BACTEC FX).ResultsIn total, 3463 surveillance cultures were performed (pharyngeal, n = 1201; axillary-rectal, n = 1200; nasal, n = 1062). MDRB colonization was documented in 122 out of 361 (33.7%) admissions corresponding to 86 patients (34.4%). A total of 149 MDRB were isolated from one or more body sites, of which most were Gram-negative bacteria, most frequently non-fermenting (n = 83) followed by Enterobacterales (n = 51). BSI were documented in 102 admissions (28%) involving 87 patients. Overall, the rate of BSI caused by MDRB was significantly higher (p = 0.04) in the presence of colonizing MDRB (16 out of 47 admissions in 14 patients) than in its absence (9 out of 55 admissions in 9 patients). Colonization by any MDRB was independently associated with increased risk of MDRB-BSI (HR, 3.70; 95% CI, 1.38–9.90; p = 0.009).ConclusionMDRB colonization is a frequent event in hematological patients hospitalized for any reason and is associated with an increased risk of MDRB BSI. The data lend support to the use of MDRB colonization surveillance cultures for predicting the occurrence of MDRB BSI in this cohort.

EpidemiologiCal POpulatioN STudy of SARS-CoV-2 in Lake CounTy, Illinois (CONTACT): Methodology and Baseline Characteristics of a Community-Based Surveillance Study.

IntroductionEpidemiologiCal POpulatioN STudy of SARS-CoV-2 in Lake CounTy, Illinois (CONTACT) is an observational, epidemiological study with a 9-month longitudinal follow-up of nonhospitalized persons aged 18 years or older currently living or employed in Lake County, IL. We describe the study design and report baseline characteristics of the study participants, including the proportion of participants with acute or previous SARS-CoV-2 infection at enrollment.MethodsAt enrollment and subsequent timepoints, participants recruited through digital and paper-based advertising campaigns reported their occupational and school-based exposure, risk factors, and behaviors, and provided nasal and serum specimens. Stratified enrichment was used to enhance enrollment into medium- and higher-risk groups within four occupational risk groups for SARS-CoV-2 infection. RT-PCR and serologic (IgG) testing were conducted to detect acute or previous SARS-CoV-2 infection in participants, respectively.ResultsBetween November 2020 and January 2021, 1008 participants (female 70.7%, mean age ± SD 51 ± 13.8 years) completed the questionnaire and diagnostic testing. Among participants, 41.8% (n = 421) were considered low risk, 24.6% (n = 248) were medium-to-low risk, 22.3% (n = 225) were medium-to-high risk, and 11.3% (n = 114) were high risk. Of 56 (5.6%) participants with evidence of acute or previous SARS-CoV-2 infection at baseline, 11 (19.6%) were RT-PCR-positive, 36 (64.3%) were IgG-seropositive, and 9 (16.1%) were positive by both assays. Participants who were adherent vs nonadherent to social distancing measures (odds ratio [95% CI] 0.8 [0.4–1.8]) were less likely, while those in higher vs lower occupational risk groups (2.0 [1.0–4.4]) were more likely to have evidence for acute or previous SARS-CoV-2 infection.ConclusionIn fall/winter 2020/21, 5.6% of adults in a Lake County convenience sample had evidence for acute or previous SARS-CoV-2 infection at baseline. Nonadherence to social distancing measures and high-risk professions were associated with SARS-CoV-2 infection. The study is ongoing and future analyses will assess infection status over time.Clinical Trial RegistrationNCT04611230.Supplementary InformationThe online version contains supplementary material available at 10.1007/s40121-022-00593-0.

In Situ Hybridization for Molecular Detection of Human Papilloma Viral 6 / 11 DNA in Adenoctomized Tissues from A group of Iraqi Pediatric Patients

Among more than 200 different human papilloma viral genotypes, the association of low oncogenic risk-HPV genotypes have been recognized with a variety of oral, oropharyngeal, nasopharyngeal benign tumors as well as non-neoplastic polyposis and papillomas and adenoid hypertrophy. This prospective case- control study aims to determine the rate of DNA detection of HPV genotype 6/11 in nasopharyngeal adeno- tonsillar tissues from a group of patients subjected to adenoctomy for adenoid hypertrophy . A total number of nasopharyngeal adeno-tonsillar tissue specimens from pediatric patients with adenoid hypertrophy were enrolled; 40 nasopharyngeal adeno-tonsillar tissues from patients with adenoid hypertrophy, and 20 normal nasal tissue specimens were obtained from pediatric patients following trimming operations of their inferior nasal turbinates' with unremarkable pathological changes (as an apparently healthy control group). The molecular detection methods for HPV detection were performed by using DNA probes via a recent version of chromogenic in situ hybridization specified for low- risk HPV genotypes. Among total adenoid hypertrophied tissue specimens group, 8 out of 40 were found to contain positive results for DNA of HPV 6 / 11 genotype, constituting 20% of the total screened nasopharyngeal adenotonsillar tissues. No positive– CISH reactions were detected in the control nasal tissues. The statistical analysis of results in this research showed significant difference when compared to the control apparently healthy tissues. The significant rate of low- oncogenic HPV genotypes detection in those adenoid hypertrophied tissues could play, in part, a role in their pathogenesis and / or constituting a herald focus for the spread of such important virally transmitted infection.