Nasal Specimens Research Articles

Factors Associated With Transmission Across Three Waves of SARS-CoV-2 in a Prospective Community-Based Study of Households With School-Aged Children-Dane County, Wisconsin, 2020-2022.

Household transmission of SARS-CoV-2 is a driver of the ongoing COVID-19 pandemic. Understanding factors that contribute to secondary infection risks (SIRs) can define changing trends and inform public health policies. The ORegon CHild Absenteeism due to Respiratory Disease Study (ORCHARDS) prospectively monitors respiratory viruses within the Oregon School District (OSD) in southcentral Wisconsin. Households with students who had ≥ 2 respiratory symptoms were eligible and opted to participate in ORCHARDS. Between October 28, 2020, and May 16, 2022, all household members provided self-collected nasal specimens on days 0, 7, and 14 for SARS-CoV-2 detection using real-time reverse-transcription-polymerase chain reaction. We used logistic regression to investigate individual- and household-level characteristics associated with SARS-CoV-2 transmission. Overall, 127 households comprising 572 individuals (48% female; 52% male; 0.4% nonbinary; 77% ≥ 18 years) had at least one detection of SARS-CoV-2. The overall SIR was 47% and decreased over time (pre-Delta = 72% [95% CI: 58%-83%]; Delta = 51% [40%-63%]; and Omicron = 41% [36%-47%]). Odds of household transmission were 63% lower during the Omicron period compared with the pre-Delta period (OR = 0.36 [95% CI: 0.13-0.94] p = 0.037). Greater household density (members/bedroom) was significantly associated with household transmission during the Omicron period (OR = 6.8, [2.19-21.37] p = 0.001). Index case age, illness severity, and individual symptoms were not significantly associated with odds of household transmission. Greater household density was associated with a higher risk of SARS-CoV-2 transmission, but the risk declined over time with subsequent variants. Interplay between variants, prior infection, and individual/household factors may identify modifiable factors (e.g., behavior and vaccination) to reduce future transmission risk.

Non-Mucosa Sparing (Reboot) Surgery as a Possible Rescue Therapy in Patients Locally Unresponsive to Biologics

Objective: Evaluation of effectiveness of non-mucosa-sparing (eg, reboot) surgery in patients with chronic rhinosinusitis with nasal polyps (CRSwNP), poorly responders to mAb therapy, who failed repeated comprehensive endoscopic surgeries. Methods: Retrospective observational study. Patients who were under mAb for a comorbid condition but still had no control over their CRSwNP were included. Data collected were preoperative tissue eosinophilia, nasal polyp score (NPS), 22-item sinonasal outcome test (SNOT-22), visual analog scale (VAS) for nasal symptoms, Lund–Kennedy score for nasal crusts (LK-c) and synechiae (LK-s), and Lund–Mackay score (LMS). The same data were also collected postoperatively (at 12 months), besides LMS, and compared. Results: Overall, 20 patients were included. Pre-reboot scores were: NPS = 4.95 ± 1.70; SNOT-22 = 63.90 ± 19.15; VAS-global = 7.06 ± 1.50; LM = 19.0 ± 4.01; LK-c = 1.10 ± 0.64; and LK-s = 1.30 ± 0.73. Tissue biopsies revealed a high density of eosinophils in all cases, ≥10/HPF (range 10-60). Mean postoperative outcomes were: NPS = 0; SNOT-22 = 17.90 ± 6.80; VAS-global = 1.91 ± 1.17; LK-c = 1.45 ± 0.51; and LK-s = 1.50 ± 0.61. The difference of mean pre- and postoperative scores was significant for both NPS, SNOT-22 and VAS-global ( P < .001). No differences were observed for LK-c and LK-s ( P > .05). Nasal specimens showed markedly reduced tissue eosinophils (100% of cases). Conclusion: Reboot sinus surgery might be an effective solution for recalcitrant CRSwNP patients unresponsive to mAbs and multiple sinus surgeries.

SARS-CoV-2 Variants from Long-Term, Persistently Infected Immunocompromised Patients Have Altered Syncytia Formation, Temperature-Dependent Replication, and Serum Neutralizing Antibody Escape.

SARS-CoV-2 infection of immunocompromised individuals often leads to prolonged detection of viral RNA and infectious virus in nasal specimens, presumably due to the lack of induction of an appropriate adaptive immune response. Mutations identified in virus sequences obtained from persistently infected patients bear signatures of immune evasion and have some overlap with sequences present in variants of concern. We characterized virus isolates obtained greater than 100 days after the initial COVID-19 diagnosis from two COVID-19 patients undergoing immunosuppressive cancer therapy, wand compared them to an isolate from the start of the infection. Isolates from an individual who never mounted an antibody response specific to SARS-CoV-2 despite the administration of convalescent plasma showed slight reductions in plaque size and some showed temperature-dependent replication attenuation on human nasal epithelial cell culture compared to the virus that initiated infection. An isolate from another patient-who did mount a SARS-CoV-2 IgM response-showed temperature-dependent changes in plaque size as well as increased syncytia formation and escape from serum-neutralizing antibodies. Our results indicate that not all virus isolates from immunocompromised COVID-19 patients display clear signs of phenotypic change, but increased attention should be paid to monitoring virus evolution in this patient population.

Characterization of Avian Influenza Viruses Detected in Kenyan Live Bird Markets and Wild Bird Habitats Reveal Genetically Diverse Subtypes and High Proportion of A(H9N2), 2018-2020.

Following the detection of highly pathogenic avian influenza (HPAI) virus in countries bordering Kenya to the west, we conducted surveillance among domestic and wild birds along the shores of Lake Victoria. In addition, between 2018 and 2020, we conducted surveillance among poultry and poultry workers in live bird markets and among wild migratory birds in various lakes that are resting sites during migration to assess introduction and circulation of avian influenza viruses in these populations. We tested 7464 specimens (oropharyngeal (OP) and cloacal specimens) from poultry and 6531 fresh fecal specimens from wild birds for influenza A viruses by real-time RT-PCR. Influenza was detected in 3.9% (n = 292) of specimens collected from poultry and 0.2% (n = 10) of fecal specimens from wild birds. On hemagglutinin subtyping, most of the influenza A positives from poultry (274/292, 93.8%) were H9. Of 34 H9 specimens randomly selected for further subtyping, all were H9N2. On phylogenetic analysis, these viruses were genetically similar to other H9 viruses detected in East Africa. Only two of the ten influenza A-positive specimens from the wild bird fecal specimens were successfully subtyped; sequencing analysis of one specimen collected in 2018 was identified as a low-pathogenicity avian influenza H5N2 virus of the Eurasian lineage, and the second specimen, collected in 2020, was subtyped as H11. A total of 18 OP and nasal specimens from poultry workers with acute respiratory illness (12%) were collected; none were positive for influenza A virus. We observed significant circulation of H9N2 influenza viruses in poultry in live bird markets in Kenya. During the same period, low-pathogenic H5N2 virus was detected in a fecal specimen collected in a site hosting a variety of migratory and resident birds. Although HPAI H5N8 was not detected in this survey, these results highlight the potential for the introduction and establishment of highly pathogenic avian influenza viruses in poultry populations and the associated risk of spillover to human populations.

Early biological markers of post-acute sequelae of SARS-CoV-2 infection

To understand the roles of acute-phase viral dynamics and host immune responses in post-acute sequelae of SARS-CoV-2 infection (PASC), we enrolled 136 participants within 5 days of their first positive SARS-CoV-2 real-time PCR test. Participants self-collected up to 21 nasal specimens within the first 28 days post-symptom onset; interviewer-administered questionnaires and blood samples were collected at enrollment, days 9, 14, 21, 28, and month 4 and 8 post-symptom onset. Defining PASC as the presence of any COVID-associated symptom at their 4-month visit, we compared viral markers (quantity and duration of nasal viral RNA load, infectious viral load, and plasma N-antigen level) and host immune markers (IL-6, IL-10, TNF-α, IFN-α, IFN-γ, MCP, IP-10, and Spike IgG) over the acute period. Compared to those who fully recovered, those reporting PASC demonstrated significantly higher maximum levels of SARS-CoV-2 RNA and N-antigen, burden of RNA and infectious viral shedding, and lower Spike-specific IgG levels within 9 days post-illness onset. No significant differences were identified among a panel of host immune markers. Our results suggest early viral dynamics and the associated host immune responses play a role in the pathogenesis of PASC, highlighting the importance of understanding early biological markers in the natural history of PASC.

Clinical Performance of the BD Respiratory Viral Panel for BD MAX™ System in Detecting SARS-CoV-2, Influenza A and B, and Respiratory Syncytial Virus

Using a nasopharyngeal (NP) or anterior nasal (NS) swab from prospectively collected or retrospective specimens, we assessed the clinical performance of the BD Respiratory Viral Panel (BD RVP) for BD MAX System against FDA-cleared or authorized comparators. Across prospective and retrospective specimens, positive percent agreement (PPA) was ≥ 98.4% for SARS-CoV-2, ≥ 96.7% for influenza (flu) A, ≥ 91.7% for respiratory syncytial virus (RSV), and 100% for flu B (retrospective only) while negative percent agreement (NPA) was ≥ 97.7% across all targets, leading to the assay FDA clearance. A head-to-head comparison of NS versus NP results with BD RVP was also performed; PPA was ≥ 90% and NPA ≥ 98.2% for SARS-CoV-2, flu A and RSV. These findings confirm that the BD MAX RVP assay performs well for detection and differentiation of the three viruses in NP and NS specimens, with strong interrater agreements for NS versus NP comparisons.

Proportions and Seasonal Patterns of Respiratory Viruses via Rapid Tests in Adults at a Greek Hospital (Oct. 2023-Mar. 2024).

Respiratory infections pose a major public health threat. The predominant viruses causing viral respiratory infections are influenza A and B (Flu-A, Flu-B), coronaviruses, respiratory syncytial virus (RSV), and adenovirus. This study aims to investigate the proportion of these cases via rapid antigen tests and assess seasonal patterns. Clinical samples were collected from symptomatic adults presenting to the Emergency and Respiratory Medicine Departments of the University Hospital of Larissa (UHL), Greece from 16 October 2023 to 31 March 2024. Nasal specimens were antigen-tested for Flu-A/B, SARS-CoV-2, RSV, and adenovirus. The total sample of specimens collected was 1434, of which 739 (51.5%) were female and 695 were male (48.5%). The mean age of participants was 57 ± 5.5 years. Among the positive results, we recorded a proportion of 40.18% and 11.40% for influenza A and B, respectively, followed by 35.79% for SARS-CoV-2, 10.70% for RSV, and 1.93% for adenovirus. In Greece, surveillance systems in infection control are underutilized. Rapid tests via multiple antigens can quickly identify viral infections, making them a valuable tool with financial benefits for health systems. Early detection of respiratory infections helps allocate resources efficiently, ensures adequate staff and facilities are available, and improves patient care through refined clinical management.

The differences between sinonasal respiratory epithelial adenomatoid hamartoma and nasal polyps: insights into immunopathology.

Respiratory epithelial adenomatoid hamartoma (REAH) is a benign lesion commonly occurring in the nasal cavity and sinuses. It is often accompanied by nasal polyps (NP). While the histological features of these two conditions have been studied, there is limited knowledge about their differences in the underlying immunopathology. Nasal tissue specimens were collected from 8 patients with concurrent REAH and NP and 10 controls. The expression levels of inflammatory cytokines, tight junctions (TJ), and epithelial-mesenchymal transition (EMT)-related factors in the tissues were analyzed. The mRNA expression of the aforementioned factors was measured using qRT-PCR, while the expression of TJ and EMT-related proteins was analyzed through Western blotting and immunohistochemistry. Compared to the control group, levels of inflammatory cytokines (IFN-α, IL-5, IL-17A, IL-31, IL-33, and TNF-α) and EMT-related factors (α-SMA, COL1A1, MMP9, TGF-β1, and Vimentin) were significantly increased in both REAH and NP tissues. Conversely, E-Cadherin and TJ-related factors (Claudin-4 and Occludin) significantly decreased. When comparing REAH with NP, it was observed that the expression of IL-4, IL-5, and IL-33 was lower in REAH, while TNF-ɑ; was higher. Regarding TJ-related factors, the expression of Occludin was lower in REAH. Furthermore, in terms of EMT-related factors, except for E-Cadherin, the expressions of ɑ-SMA, COL1A1, CTGF, MMP9, TGF-β11, and Vimentin were higher in REAH. REAH and NP exhibit different immunopathological mechanisms. NP demonstrates a more severe inflammatory response, whereas REAH is characterized by a more pronounced TJ and EMT breakdown than NP.

The nasal microbiota is a potential diagnostic biomarker for sepsis in critical care units.

This study aimed to characterize the composition of intestinal and nasal microbiota in septic patients and identify potential microbial biomarkers for diagnosis. A total of 157 subjects, including 89 with sepsis, were enrolled from the affiliated hospital. Nasal swabs and fecal specimens were collected from septic and non-septic patients in the intensive care unit (ICU) and Department of Respiratory and Critical Care Medicine. DNA was extracted, and the V4 region of the 16S rRNA gene was amplified and sequenced using Illumina technology. Bioinformatics analysis, statistical processing, and machine learning techniques were employed to differentiate between septic and non-septic patients. The nasal microbiota of septic patients exhibited significantly lower community richness (P = 0.002) and distinct compositions (P = 0.001) compared to non-septic patients. Corynebacterium, Staphylococcus, Acinetobacter, and Pseudomonas were identified as enriched genera in the nasal microbiota of septic patients. The constructed machine learning model achieved an area under the curve (AUC) of 89.08, indicating its efficacy in differentiating septic and non-septic patients. Importantly, model validation demonstrated the effectiveness of the nasal microecological diagnosis prediction model with an AUC of 84.79, while the gut microecological diagnosis prediction model had poor predictive performance (AUC = 49.24). The nasal microbiota of ICU patients effectively distinguishes sepsis from non-septic cases and outperforms the gut microbiota. These findings have implications for the development of diagnostic strategies and advancements in critical care medicine.IMPORTANCEThe important clinical significance of this study is that it compared the intestinal and nasal microbiota of sepsis with non-sepsis patients and determined that the nasal microbiota is more effective than the intestinal microbiota in distinguishing patients with sepsis from those without sepsis, based on the difference in the lines of nasal specimens collected.

Association of Symptoms and Viral Culture Positivity for SARS-CoV-2-Tennessee, April-July 2020.

Understanding how symptoms are associated with SARS-CoV-2 culture positivity is important for isolation and transmission control guidelines. Individuals acutely infected with SARS-CoV-2 in Tennessee and their household contacts were recruited into a prospective study. All participants self-collected nasal swabs daily for 14 days and completed symptom diaries from the day of illness onset through day 14 postenrollment. Nasal specimens were tested for SARS-CoV-2 using RT-qPCR. Positive specimens with cycle threshold values < 40 were sent to the Centers for Disease Control and Prevention (CDC) for viral culture. First, we modeled the association between symptoms and the risk of culture positivity using an age-adjusted generalized additive model (GAM) accounting for repeated measurements within participants and a symptom-day spline. Next, we investigated how timing of symptom resolution was associated with the timing of culture resolution. In a GAM restricted to follow-up days after symptoms began, the odds of a specimen being culture positive was significantly increased on days when wheezing, loss of taste or smell, runny nose, nasal congestion, sore throat, fever, or any symptom were reported. For all symptoms except sore throat, it was more common for participants to have culture resolution before symptom resolution than for culture to resolve after or on the same day as symptom resolution. Overall, symptomatic individuals were more likely to be SARS-CoV-2 viral culture positive. For most symptoms, culture positivity was more likely to end before symptoms resolved. However, a proportion of individuals remained culture positive after symptom resolved, across all symptoms.

Surveillance and phylogenetic analysis of a pathogenic bacterium candidate in nasal discharge from children.

"The infectious organism lurking in human airways (IOLA)" is a candidate pathogenic bacterium detected in bronchoalveolar lavage fluid specimens derived from adult patients with chronic lower respiratory tract infections. Genomic analyses of IOLA have revealed that it possesses the smallest and most AT-rich genome among human-derived bacteria. However, its biological properties remain unclear because no culture method has been established for IOLA. Here, we conducted a large-scale IOLA surveillance study of nasal discharge specimens from children in Japan and investigated the correlation between IOLA detection frequency and patient characteristics. We detected IOLA in 5.4% (103 of 1,920) of pediatric nasal discharge samples. No significant differences were observed in the frequency of detection based on the patient's background. However, with respect to age, the frequency of detection tended to be significantly high at 2-3 and 6 years old. Phylogenetic analysis revealed five phylotypes in the IOLA 16S rRNA gene sequences, and the sequences detected in adult patients with respiratory infections in a previous study belonged to one of the five phylotypes. The involvement of IOLA in the symptoms is not clear, but IOLA is detected at a relatively high frequency in pediatric nasal discharge. Many subjects with detected IOLA were not always IOLA positive, and IOLA was detected transiently. Our findings suggest that IOLA is horizontally transmitted through groups in nursery and elementary schools, and there are differences in biological characteristics among the IOLA phylotypes.IMPORTANCE"The infectious organism lurking in human airways (IOLA)" is a candidate pathogenic bacterium strongly suspected to be infectious to the respiratory tracts of humans and animals. However, a culture method for IOLA has not been established yet, and its properties remain unclear. In this study, IOLA was detected at a relatively high frequency in the nasal discharge of children, and five phylotypes of IOLA were identified. One of these phylotypes was found in the bronchoalveolar lavage fluid from adult patients, suggesting lineage-specific differences in the pathogenicity of IOLA. Moreover, it was suggested that IOLA is horizontally transmitted when children gather in groups such as nursery and elementary schools. These findings strongly indicate that IOLAs have been clinically undetected so far but are spreading among children, with one lineage being involved in respiratory diseases in adults. Examining the presence of IOLA in clinical specimens may help to understand the etiology of respiratory diseases with unknown causes.

The preliminary application of mNGS in the diagnosis of invasive fungal sinusitis

Objective: By conducting a retrospective analysis of the clinical data of 14 patients diagnosed with invasive fungal rhinosinusitis (IFRS) confirmed by metagenomics next generation sequencing (mNGS) technology, we aim to explore the rapid diagnosis value of mNGS in IFRS. Methods: The clinical data of 14 IFRS patients admitted to TianJin First Central Hospital were retrospectively analyzed from February 2021 to October 2023. The study cohort comprised 8 males and 6 females, with ages ranging from 14 to 77 years. All patients were diagnosed as IFRS by performing mNGS sequencing technology of nasal sinus lesion biopsy specimens. Clinical data such as laboratory examination, imaging examination, histopathological examination results, treatment plan and prognosis were summarized and analyzed. Results: All 14 patients were diagnosed as IFRS, with mNGS detecting pathogens such as Rhizopus (7 cases), Aspergillus (5 cases), Trichoderma (1 case), and Scedosporium apiospermum (1 case). Follow-up evaluations were conducted for a period ranging from 2 months to 2 years post-treatment. At the end of follow-up, 11 out of 14 IFRS patients achieved a complete cure with no signs of recurrence, while the symptoms of the remaining 3 patients significantly improved with comprehensive treatment. Conclusion: mNGS emerges as a highly effective diagnostic tool for IFRS, providing valuable microbiological evidence for clinical diagnosis and demonstrating promising clinical utility.

Association of mucus eosinophil-derived neurotoxin levels with disease control status in patients with chronic rhinosinusitis.

Identifying the biomarkers for uncontrolled chronic rhinosinusitis (CRS) is important for directing treatment decisions. Eosinophilia has been reported to be involved in the poor disease control of CRS and mucus eosinophil-derived neurotoxin (EDN) is potentially a biomarker of intense eosinophil activation. This study aimed to assess the relationship between mucus EDN levels, disease severity, and degree of CRS control. A total of 150 adult patients with CRS and 25 healthy controls were prospectively enrolled. The nasal mucus and tissue specimens were collected to analyze EDN levels. Disease severity was assessed by Lund-Mackay score and 22-item Sino-Nasal Outcome Test (SNOT-22) score. Five CRS symptom severities during the prior month (nasal blockage, rhinorrhoea/postnasal drip, facial pain/pressure, smell, sleep disturbance or fatigue), use of rescue medications in the last six months, and the presence of diseased mucosa on nasal endoscopy were obtained. Consistent with the European Position Paper on Rhinosinusitis and Nasal Polyps 2020 CRS control criteria, uncontrolled CRS was defined as meeting at least three items. 40% of patients with CRS presented with uncontrolled status. Patients with uncontrolled CRS had significantly higher nasal mucus EDN levels (P = 0.010), percentage of blood eosinophil (P = 0.015), SNOT-22 score (P < 0.001), Lund-Mackay score (P = 0.008), and a more eosinophilic dominant phenotype of CRS (P < 0.001) than patients with controlled CRS. Furthermore, mucus EDN levels were positively correlated with blood eosinophils (r = 0.541, P = 0.005), SNOT-22 score (r = 0.460, P = 0.021), and Lund-Mackay score (r = 0.387, P = 0.039). Mucus EDN levels were the significant parameter related to uncontrolled CRS in multivariable analysis after adjusting for patient demographics and comorbidities (odds ratio = 1.323; P = 0.004). Mucus EDN levels may be a potential biomarker for identifying the CRS control status.

C-reactive Protein Kinetics During In-Patient Treatment of COVID-19-Associated Rhino-Orbito-Cerebral Mucormycosis: A Retrospective Cohort Study in a Tertiary Hospital in Central India.

COVID-associated rhino-orbito-cerebral Mucormycosis (CA-ROCM), henceforth referred to as Covid-Associated Mucormycosis (CAM), is a serious and fatal condition unless treated promptly and completely. The main treatment of the CAM is complete surgical debridement and administration of systemic antifungals. The first line antifungal recommended for CAM is Amphotericin-B. Since Amphotericin-B has systemic side effects mainly on the renal system, a timely decision to start and end Amphotericin-B therapy is very essential. Besides the Computed Tomography (CT) scan, serum levels of C-reactive protein (CRP) levels are a good indicator of CAM-associated inflammation levels in the patient's body. By monitoring the CRP levels, we can titrate amphotericin treatment to cause minimal harm to the kidneys.Our study was done to analyze the kinetics of C-reactive protein in patients of CAM admitted in a tertiary-care hospital and compare it with the CRP levels in COVID-associated non-Mucormycosis Sinusitis patients. Aim and objective To study the kinetics of serum C-reactive protein (CRP) levels among patients undergoing in-patient care for COVID-associated rhino-orbito-cerebral mucormycosis and compare with serum CRPlevels in COVID-19 patients suffering from sinusitis without rhino-orbito-cerebral mucormycosis. Materials and methods This was a retrospective cohort study. The source of data was post-COVID sinusitis patients who were admitted during 2nd wave of COVID-19 in India in our hospital whose medical records were accessed by the Medical Records Department. The subjects were recruited into the two study groups namely the Mucormycosis group and the non-Mucormycosis group based on the histopathological report of the nasal biopsy specimen. The medical records of each member of the two groups were studied for the levels of serum C-reactive protein measured at the time of admission and every 5(+1) days thereafter till the time of discharge. The kinetics of serum C-reactive protein levels, which is a marker of inflammation is studied in each of the two groups and compared using statistical methods. Results There was a significant difference between Mucormycosis and Non-Mucormycosis groups in CRP-level kinetics. However, there was no significant trend of decrease or increase over time in Mucormycosis as well as non-Mucormycosis cases. Conclusion CRP is an important biomarker in assessing the septic response to COVID-associated rhino-orbito-cerebral mucormycosis. Detection of raised CRP levels helps in prompt early initiation of anti-fungal treatment. Also, monitoring the levels of serum CRP will guide in deciding the time to stop the antifungals at an appropriate time. CRP monitoring is commonly available and affordable. Hence, we recommend CRP monitoring of in-patients of CAM.

Prevalence, Patterns, and Predictors of SARS-CoV-2 RNA and Culturable Virus in Tears of a Case-Ascertained Household Cohort

To investigate the prevalence, patterns, and predictors of SARS-CoV-2 RNA and culturable virus in tears of a case-ascertained household cohort. Prospective, longitudinal case-ascertained household cohort identified through convenience sampling. This analysis was restricted to individuals who were non-hospitalized, symptomatic, and tested positive for SARS-CoV-2 by nasal RT-PCR. Tears and anterior nasal biospecimens were serially collected throughout the acute period. Tears specimens were collected by the study staff using Schirmer test strips, and nasal specimens were self-collected. For both, SARS-CoV-2 RNA was quantified using qRT-PCR, and culturable virus was detected using presence of cytopathic effect (CPE) in tissue culture; positive CPE was confirmed by a qRT-PCR step. A series of cross-sectional unadjusted analyses were performed investigating the relationship between different sociodemographic determinants and biological factors associated with tears RNA positivity. Among the 83 SARS-CoV-2 infected participants, 10 (12%) had at least one RNA-positive tears specimen. Amongst these 10, 5 (50%) had concurrent presence of culturable virus, at a median of 7 days postsymptom onset (IQR: 4-7 days) (absolute range: 4-8 days). In this longitudinal cohort, we found evidence of culturable virus in the tears of a small proportion of nonhospitalized SARS-CoV-2 infected individuals. Current public health infection precautions do not account for transmission via tears, so these findings may improve our understanding of potential sources of SARS-CoV-2 transmission and contribute to developing future guidelines.

High SARS-CoV-2 attack rates in areas with low detection after community transmission established in Port Vila, Vanuatu, April 2022.

On 4 March 2022, the first community-acquired case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in Vanuatu, with community transmission occurring subsequently. It was expected that the number of notified SARS-CoV-2 cases would be an underestimate of the true infection rate of this outbreak; however, the magnitude of underreporting was unknown. The purpose of this study was to provide a population-based estimate of SARS-CoV-2 infection shortly after the first reports of community transmission, to understand the level of underdetection and undernotification in Vanuatu and thus to inform ongoing prevention and response activities. We conducted a cross-sectional SARS-CoV-2 prevalence study in two geographical administrative areas in Port Vila, Vanuatu in April 2022. All residents in selected areas were eligible. Trained teams conducted demographic and behavioural interviews and collected nasal specimens. Specimens were tested by polymerase chain reaction. The primary outcomes were the rates of SARS-CoV-2 attack (point prevalence) and cumulative attack, underdetection, notification and household secondary attack. A total of 252 people from 84 households participated. Among 175 people who had a sample collected, 91 were SARS-CoV-2-positive (attack rate 52.0%). Most cases had not been detected before the study (underdetection rate 91.5%). More than half of previously detected cases were notified (notification rate 65.2%). Within the first few weeks of community transmission, more than half of participants in the selected areas had evidence of SARS-CoV-2 infection; however, most infections had been undetected. This study provides important information about the rapid spread of novel infectious diseases in Vanuatu.

Abstract 4781: Evaluation of a TP53 biomarker for lung cancer risk in nasal brushings and peripheral blood

Abstract Background and Purpose: Early detection of lung cancer through annual screening with low-dose computed tomography (LDCT) scans enables potentially curative surgical or stereotactic body radiation therapy (SBRT) treatment and thereby significantly reduces mortality. However, LDCT screening among those currently eligible based primarily on age and smoking criteria yields a large number of false-positive findings and many lung cancers occur among individuals who currently are ineligible. A biomarker that identifies lung cancer risk independent from that caused by age and cigarette smoking might increase specificity and increase the number of people eligible for LDCT screening. Recently we demonstrated that a biomarker measuring TP53 somatic mutations in bronchial brush biopsy specimens from grossly normal airway epithelium was significantly associated with cancer status independent of age and smoking status. Additionally, the TP53 biomarker was synergistic with traditional risk score models (e.g. PLCOM2012 risk score). The goal of this pilot study was to test the TP53 biomarker in nasal brush biopsy specimens, a potential surrogate tissue obtained using less invasive collection methods. Methods: Nasal brushings from 10 lung cancer and 11 control subjects were collected at the University of Toledo and Vanderbilt University Medical Center under approved institutional protocols. Genomic DNA (gDNA) was extracted with the Qiagen AllPrep DNA/RNA kit using a modified protocol. Amplifiable copies of gDNA were measured using quantitative PCR. For each test a sample comprising 25,000 amplifiable copies of gDNA was combined with 50,000 copies of a TP53 internal standard and a complexity control, then PCR amplified, purified and barcoded. Samples were pooled to create two NGS libraries, each with approximately equal numbers of cases and controls, and sequenced on an Illumina MiSeq (Two V3 flow cells, 2 x 250 paired-end). Bioinformatic analysis was conducted using Qiagen CLC Workbench. Variants were called using the Basic Variant Detection Tool. Poisson Exact Test was utilized to determine the significance of endogenous variants relative to internal standard variants at the same base position and a Bonferroni correction was applied to minimize false discovery. Comparison of variant numbers between cases and controls was conducted using an f-test followed by a paired t-test. Results and Conclusions: Consistent with previous results in airway epithelium, in this pilot study the TP53 mutation biomarker measured in nasal brushing was associated with lung cancer (p=0.0085). Measurement of the TP53 biomarker in nasal brush specimens in a larger case-control study currently is underway along with a pilot study in gDNA from peripheral blood. Citation Format: Erin L. Crawford, Daniel J. Craig, Patrick T. Gorman, Mohamed Omballi, Rami Ahmad, Eric L. Grogan, Stephen A. Deppen, James C. Willey. Evaluation of a TP53 biomarker for lung cancer risk in nasal brushings and peripheral blood [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4781.

Clinical and laboratory characteristics of patients hospitalized with severe COVID-19 in New Orleans, August 2020 to September 2021

Louisiana experienced high morbidity and mortality from COVID-19. To assess possible explanatory factors, we conducted a cohort study (ClinSeqSer) of patients hospitalized with COVID-19 in New Orleans during August 2020–September 2021. Following enrollment, we reviewed medical charts, and performed SARS-CoV-2 RT-PCR testing on nasal and saliva specimens. We used multivariable logistic regression to assess associations between patient characteristics and severe illness, defined as ≥ 6 L/min oxygen or intubation. Among 456 patients, median age was 56 years, 277 (60.5%) were Black non-Hispanic, 436 (95.2%) had underlying health conditions, and 358 were unvaccinated (92.0% of 389 verified). Overall, 187 patients (40.1%) had severe illness; 60 (13.1%) died during admission. In multivariable models, severe illness was associated with age ≥ 65 years (OR 2.08, 95% CI 1.22–3.56), hospitalization > 5 days after illness onset (OR 1.49, 95% CI 1.01–2.21), and SARS CoV-2 cycle threshold (Ct) result of < 32 in saliva (OR 4.79, 95% CI 1.22–18.77). Among patients who were predominantly Black non-Hispanic, unvaccinated and with underlying health conditions, approximately 1 in 3 patients had severe COVID-19. Older age and delayed time to admission might have contributed to high case-severity. An association between case-severity and low Ct value in saliva warrants further investigation.

Longitudinal Molecular and Serological Evidence of SARS-CoV-2 Infections and Vaccination Status: Community-Based Surveillance Study (CONTACT).

This prospective, longitudinal, community-based study,EpidemiologiCal POpulatioN STudy of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Lake CounTy, Illinois(CONTACT), investigated coronavirus disease 2019 (COVID-19) immunity, occupational risks related to SARS-CoV-2 exposure, and long-term immunoglobulin G (IgG) seroconversion kinetics. At baseline and follow up (3, 6, and 9months), non-hospitalized adult participants provided nasal and blood serum specimens for molecular [reverse transcription polymerase chain reaction (RT-PCR)] and serological (IgG) testing (4 November 2020-30 October 2021). At baseline, 6.4% (65/1008) had evidence of current/prior SARS-CoV-2 infection. At 3, 6, and 9months, positive PCR tests were obtained from 0.4% (3/781), 0.4% (3/733), and 0% (0/673) of participants, respectively. Positive IgG occurred at baseline and 3, 6, and 9months in 4.5% (45/1008), 6.0% (48/799), 5.4% (39/733), and 2.8% (19/673) of participants, respectively. Of participants positive for IgG at baseline, 28 had a negative IgG test at a follow-up visit; of those 28, 21 had their first negative IgG test within 6months. Participants were more likely to retain positive IgG if they were 18-29years of age, were male, or had medium-high/high-risk occupations. A high vaccination rate (70% received ≥ 1 dose by 9months) was observed. Influence of occupational status or characteristics on transmission and IgG, and COVID-19 vaccination trends, are shown. This study expands on prior studies assessing COVID-19 immunity and IgG seroconversion by including both RT-PCR and serologic testing and longitudinal follow-up of study participants. We observed decreased infection rates over the 9month follow-up period as well as a decline in IgG persistency after 6months. The findings from this community-based study regarding vaccinate rates, infection rates by PCR, and IgG persistency over time can help improve our understanding of COVID-19 immunity, occupational risks related to SARS-CoV-2 exposure, and the kinetics of long-term IgG seroconversion, which is important to help guide local and national mitigation strategies. NCT04611230.

A new software for automated analysis of respiratory tract ciliary epithelium movement for the diagnosis of primary ciliary dyskinesia

Primary ciliary dyskinesia (PCD) is a rare hereditary disease. In this ciliopathy, the disturbed structure and motility of the ciliary epithelium negatively affects the ciliary function and leads to prominent decrease or absence of mucociliary clearance. The European guidelines recommend analyzing the cilia beat frequency (СBF) in a native preparation or in ALI culture using light microscopy as one of the methods to confirm the diagnosis of PCD.The aim of this project was to create software for automated analysis of the movement/beating of the ciliary epithelium of the respiratory tract for the diagnosis of primary ciliary dyskinesia using digital high-speed video microscopy in vivo and in vitro.Methods. Five healthy donors and 10 patients with suspected PCD underwent nasal epithelial brush biopsy. The preparations were examined with a transmission electron microscope in vivo. Epithelial cells were also isolated from the nasal biopsy specimen, and ciliogenesis of these cells was performed by ALI-culturing, followed by digital high-speed video microscopy and assessment of the number of active cells and cilia beating frequency. The resulting video images were used to create the software.Results. Software for determination of ciliary epithelium beat frequency in primary ciliary dyskinesia (PCD HighSpeed Video Microscopy Analysis – PCD HSVMA) was created to optimize the diagnosis of PCD by light microscopy (software registration number 2023687245). The software is designed to count the number of active cells of ciliary epithelium and CBF (Hz) by digital high-speed video microscopy in vivo and in vitro in ALI-culture. PCD HSVMA software features storage of patient data, display of heat map, formation of a large server database of patients and video files, building of color and static histograms, processing of several areas in one video. Our software has a number of advantages over CiliarMove and Cilialyzer and has high correlation of CFB (Hz) estimation with these products.Conclusion. Our software can be used for improvement of PCD diagnostics in laboratories of healthcare institutions, in scientific institutions and can be included in specialist educational programs for laboratory doctors, pediatricians, general practitioners, pulmonologists, diagnosticians (endoscopists).