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As the SARS‐CoV‐2 virus spread throughout the world, millions of positive cases of COVID‐19 were registered and, even though there are millions of people already vaccinated against SARS‐CoV‐2, a large part of the global population remains vulnerable to contracting the virus. Massive nasopharyngeal sample collection in Puerto Rico at the beginning of the pandemic was limited by the scarcity of trained personnel and testing sites. To increase SARS‐CoV‐2 molecular testing availability, we evaluated the diagnostic accuracy of self‐collected nasal, saliva, and urine samples using the TaqPath reverse transcription polymerase chain reaction (RT‐PCR) COVID‐19 kit to detect SARS‐CoV‐2. We also created a colorimetric loop‐mediated isothermal amplification (LAMP) laboratory developed test (LDT) to detect SARS‐CoV‐2, as another strategy to increase the availability of molecular testing in community‐based laboratories. Automated RNA extraction was performed in the KingFisher Flex instrument, followed by PCR quantification of SARS‐CoV‐2 on the 7500 Fast Dx RT‐PCR using the TaqPath RT‐PCR COVID‐19 molecular test. Data was interpreted by the COVID‐19 Interpretive Software from Applied Biosystems and statistically analyzed with Cohen's kappa coefficient (k). Cohen's kappa coefficient (k) for paired nasal and saliva samples showed moderate agreement (0.52). Saliva samples exhibited a higher viral load. We also observed 90% concordance between LifeGene‐Biomarks' SARS‐CoV‐2 Rapid Colorimetric LAMP LDT and the TaqPath RT‐PCR COVID‐19 test. Our results suggest that self‐collected saliva is superior to nasal and urine samples for COVID‐19 testing. The results also suggest that the colorimetric LAMP LDT is a rapid alternative to RT‐PCR tests for the detection of SARS‐CoV‐2. This test can be easily implemented in clinics, hospitals, the workplace, and at home; optimizing the surveillance and collection process, which helps mitigate global public health and socioeconomic upheaval caused by airborne pandemics. [ABSTRACT FROM AUTHOR]

Little information is presently available regarding the frequency of the silent shedders of respiratory viruses in healthy sport horses and their impact on environmental contamination. Therefore, the aim of this study was to investigate the detection frequency of selected respiratory pathogens in nasal secretions and environmental stall samples of sport horses attending a multi-week equestrian event during the summer months. Six out of fifteen tents were randomly selected for the study with approximately 20 horse/stall pairs being sampled on a weekly basis. Following weekly collection for a total of 11 weeks, all samples were tested for the presence of common respiratory pathogens (EIV, EHV-1, EHV-4, ERAV, ERBV, and Streptococcus equi ss equi (S. equi)) using qPCR. A total of 19/682 nasal swabs (2.8%) and 28/1288 environmental stall sponges (2.2%) tested qPCR-positive for common respiratory pathogens. ERBV was the most common respiratory virus (17 nasal swabs, 28 stall sponges) detected, followed by EHV-4 (1 nasal swab) and S. equi (1 nasal swab). EIV, EHV-1, EHV-4 and ERAV were not detected in any of the study horses or stalls. Only one horse and one stall tested qPCR-positive for ERBV on two consecutive weeks. All the other qPCR-positive sample results were related to individual time points. Furthermore, only one horse/stall pair tested qPCR-positive for ERBV at a single time point. The study results showed that in a selected population of sport horses attending a multi-week equestrian event in the summer, the frequency of the shedding of respiratory viruses was low and primarily restricted to ERBV with little evidence of active transmission and environmental contamination.

BackgroundIdentifying characteristics associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA shedding may be useful to understand viral compartmentalization, disease pathogenesis, and risks for viral transmission.MethodsParticipants were enrolled August 2020 to February 2021 in ACTIV-2/A5401, a placebo-controlled platform trial evaluating investigational therapies for mild-to-moderate coronavirus disease 2019 (COVID-19), and underwent quantitative SARS-CoV-2 RNA testing on nasopharyngeal and anterior nasal swabs, oral wash/saliva, and plasma at entry (day 0, pretreatment) and days 3, 7, 14, and 28. Concordance of RNA levels (copies/mL) across compartments and predictors of nasopharyngeal RNA levels were assessed at entry (n = 537). Predictors of changes over time were evaluated among placebo recipients (n = 265) with censored linear regression models.ResultsNasopharyngeal and anterior nasal RNA levels at study entry were highly correlated (r = 0.84); higher levels of both were associated with greater detection of RNA in plasma and oral wash/saliva. Older age, White non-Hispanic race/ethnicity, lower body mass index (BMI), SARS-CoV-2 immunoglobulin G seronegativity, and shorter prior symptom duration were associated with higher nasopharyngeal RNA at entry. In adjusted models, body mass index and race/ethnicity associations were attenuated, but the association with age remained (for every 10 years older, mean nasopharyngeal RNA was 0.27 log10 copies/mL higher; P < .001). Examining longitudinal viral RNA levels among placebo recipients, women had faster declines in nasopharyngeal RNA than men (mean change, -2.0 vs -1.3 log10 copies/mL, entry to day 3; P < .001).ConclusionsSARS-CoV-2 RNA shedding was concordant across compartments. Age was strongly associated with viral shedding, and men had slower viral clearance than women, which could explain sex differences in acute COVID-19 outcomes.

• α-diversity and evenness were higher in nasal lavage compared to nose swabs. • Only microbiome in nasal lavage correlated with upper airway inflammation. • Abundance of Moraxella was associated with higher inflammation in the upper airways. Cystic fibrosis (CF) is characterized by highly viscous mucus obstructing the lower and upper airways, chronic neutrophil inflammation and infection resulting not only in lung destruction but also in paranasal sinus involvement. The pathogenesis of CF-associated chronic rhinosinusitis (CRS) is still not well understood, and it remains unclear how the microbiome in the upper airways (UAW) influences paranasal sinus inflammation. In a cross-sectional study in pediatric patients with CF under stable disease conditions, we examined the microbiome in relation to inflammation by comparing nasal swabs (NS) and nasal lavage (NL) as two UAW sampling methods. The microbiota structure of both NS and NL was determined by 16S rRNA gene amplicon sequencing. In addition, pro-inflammatory cytokines (IL-1β, IL-6, IL-8, TNF-α) and proteases (SLPI, TIMP-1, NE/A1-AT complex) as well as neutrophil elastase activity were measured in NL. Simultaneous NS and NL samples were collected from 36 patients with CF (age range: 7 – 19 years). The microbiome of NS samples was shown to be significantly lower in α-diversity and evenness compared to NL samples. NS samples were particularly found to be colonized with Staphylococcus species. NL microbiome was shown to correlate much better with the sinonasal inflammation status than NS microbiome. Especially the detection of Moraxella in NL was associated with increased inflammatory response. Our results show that the NL microbiome reflects sinonasal inflammation better than NS and support NL as a promising tool for simultaneous assessment of the UAW microbiome and inflammation in children with CF. [ABSTRACT FROM AUTHOR]

Background Respiratory viral shedding is incompletely characterized by existing studies due to the lack of longitudinal nasal sampling and limited inclusion of healthy/asymptomatic children. We describe characteristics associated with prolonged virus detection by polymerase chain reaction (PCR) in a community-based birth cohort. Methods Children were followed from birth to 2 years of age in the PREVAIL cohort. Weekly nasal swabs were collected and tested using the Luminex Respiratory Pathogen Panel. Weekly text surveys were administered to ascertain the presence of acute respiratory illnesses defined as fever and/or cough. Maternal reports and medical chart abstractions identified healthcare utilization. Prolonged virus detection was defined as a persistently positive test lasting ≥4 weeks. Factors associated with prolonged virus detection were assessed using mixed effects multivariable logistic regression. Results From a sub-cohort of 101 children with ≥70% weekly swabs collected, a total of 1489 viral infections were detected. Prolonged virus detection was found in 23.4% of viral infections overall, 39% of bocavirus infections, 33% of rhinovirus/enterovirus infections, 14% of respiratory syncytial virus (RSV) A infections, and 7% of RSV B infections. No prolonged detection was found for influenza virus A or B, coronavirus 229E or HKU1, and parainfluenza virus 2 or 4 infections. First-lifetime infection with each virus, and co-detection of another respiratory virus were significantly associated with prolonged detection, while symptom status, child sex, and child age were not. Conclusions Prolonged virus detection was observed in 1 in 4 viral infections in this cohort of healthy children and varied by pathogen, occurring most often for bocavirus and rhinovirus/enterovirus. Evaluating the immunological basis of how viral co-detections and recurrent viral infections impact duration of virus detection by PCR is needed to better understand the dynamics of prolonged viral shedding. [ABSTRACT FROM AUTHOR]

Abstract As the SARS‐CoV‐2 virus spread throughout the world, millions of positive cases of COVID‐19 were registered and, even though there are millions of people already vaccinated against SARS‐CoV‐2, a large part of the global population remains vulnerable to contracting the virus. Massive nasopharyngeal sample collection in Puerto Rico at the beginning of the pandemic was limited by the scarcity of trained personnel and testing sites. To increase SARS‐CoV‐2 molecular testing availability, we evaluated the diagnostic accuracy of self‐collected nasal, saliva, and urine samples using the TaqPath reverse transcription polymerase chain reaction (RT‐PCR) COVID‐19 kit to detect SARS‐CoV‐2. We also created a colorimetric loop‐mediated isothermal amplification (LAMP) laboratory developed test (LDT) to detect SARS‐CoV‐2, as another strategy to increase the availability of molecular testing in community‐based laboratories. Automated RNA extraction was performed in the KingFisher Flex instrument, followed by PCR quantification of SARS‐CoV‐2 on the 7500 Fast Dx RT‐PCR using the TaqPath RT‐PCR COVID‐19 molecular test. Data was interpreted by the COVID‐19 Interpretive Software from Applied Biosystems and statistically analyzed with Cohen's kappa coefficient (k). Cohen's kappa coefficient (k) for paired nasal and saliva samples showed moderate agreement (0.52). Saliva samples exhibited a higher viral load. We also observed 90% concordance between LifeGene‐Biomarks' SARS‐CoV‐2 Rapid Colorimetric LAMP LDT and the TaqPath RT‐PCR COVID‐19 test. Our results suggest that self‐collected saliva is superior to nasal and urine samples for COVID‐19 testing. The results also suggest that the colorimetric LAMP LDT is a rapid alternative to RT‐PCR tests for the detection of SARS‐CoV‐2. This test can be easily implemented in clinics, hospitals, the workplace, and at home; optimizing the surveillance and collection process, which helps mitigate global public health and socioeconomic upheaval caused by airborne pandemics.

Isolation of high quality and quantity genomic DNA is essential for molecular studies. It is crucial to select a non-invasive and straightforward technique to ensure the efficient collection of DNA, particularly at the farm level. The aim of this study was to determine if nasal swabs are an appropriate biological matrix to obtain good quality genomic DNA suitable for SNP genotyping. In this study, two biological matrices (blood and nasal swabs) were evaluated and compared for the isolation of genomic DNA obtained from 15 female Texel sheep. DNA quality and quantity were assessed using spectrophotometry and gel electrophoreses. Genotype concordance rates were used for comparison. Results showed that the highest concentration mean was obtained from blood samples (159.14 ng/µl), while from nasal swab samples the concentration mean was lower (130.12 ng/µl), but the difference was non-significant. Regarding purity, DNA obtained from nasal swabs presented a higher A260/A280 ratio (1.96), while the one obtained from blood samples was 1.90. Total DNA yield obtained from blood samples (15.91 µg) was significantly higher than the one obtained from nasal swabs (6.51). Blood and nasal swab genotyping concordance rates were high (mean = 0.984). In conclusion, our results indicate that nasal swabs can yield good quality DNA; however, the DNA extraction protocol should be optimized.

The virus discovered in 2019 in the city of Wuhan, China, which was later identified as SARS-CoV-2 and which spread to the level of a pandemic, put diagnostic methods to the test. Early in the pandemic, we developed a nested PCR assay for the detection of SARS-CoV-2, which we validated and applied to detect the virus in feline samples. The present study describes the application of the nested PCR test in parallel with LAMP for the detection of the virus in 427 nasopharyngeal and oropharyngeal human samples taken between October 2020 and January 2022. Of the swabs tested, there were 43 positives, accounting for 10.1% of all samples tested, with the negatives numbering 382, i.e., 89.5%, and there were 2 (0.4%) invalid ones. The nPCR results confirmed those obtained by using LAMP, with results concordant in both methods. Nasal swabs tested using nPCR confirmed the results of oropharyngeal and nasopharyngeal swab samples tested using LAMP and nPCR. The focus of the discussion is on the two techniques: the actual practical application of the laboratory-developed assays and the diagnostic value of nasal samples. The nPCR used is a reliable and sensitive technique for the detection of SARS-CoV-2 in nasopharyngeal, oropharyngeal, and nasal swab samples. However, it has some disadvantages related to the duration of the entire process, as well as a risk of contamination. Experiments were performed to demonstrate the infectivity of the virus from the positive isolates in vitro. A discrepancy was reported between direct and indirect methods of testing the virus and accounting for its ability to cause infection in vitro. [ABSTRACT FROM AUTHOR]

Usage of self‐screening tests has become increasingly relevant in public health perspective for early detection of SARS‐CoV‐2 infection in the transitioning era of the COVID‐19 pandemic into an endemic. This study was designed to compare the diagnostic accuracy of self‐conducted and health professional‐conducted SARS‐CoV‐2 rapid antigen tests (Ag‐RDTs) and whether the sample was taken from anterior nasal or nasal mid‐turbinate. Eligible comparative Ag‐RDTs accuracy studies were retrieved from electronic databases systematically, in accordance with PRISMA. Selected studies were assessed for risk of bias using QUADAS‐2 and QUADAS‐C. In total, we selected five out of 1952 studies retrieved using the keywords. The overall sensitivity for the self‐collected nasal swab method and healthcare worker‐collected nasopharyngeal swab method was 79% (95% CI 68–87; I2 = 62%) and 83% (95% CI 75–89; I2 = 32%), respectively, which was not statistically different (p = 0.499). Nasal mid‐turbinate swabs have a significantly higher sensitivity compared to anterior nasal swabs (p < 0.01). Both sampling methods represent high and comparable specificity values of 98% (95% CI 97–99; I2 = 0%) and 99% (95% CI 98–99; I2 = 0%). Positive predictive value (range 90%–99%) and negative predictive value (range 87%–98%) were equivalent for both methods. Our findings indicated the accuracy of self‐collected Ag‐RDT on nasal swabs was comparable to those performed by healthcare worker‐collected on nasopharyngeal swabs. Self‐collected Ag‐RDT could be considered as a transmission prevention method in the transition of COVID‐19 pandemic. [ABSTRACT FROM AUTHOR]

The aim of this study was to characterize the occupational exposure to inhalable dust and airborne fungi among archive and library workers based on qualitative and quantitative analyses of stationary and personal filter samples as well as nasal swabs. The study was carried out in 3 archives and 2 libraries and involved 9 workers of these institutions. Airborne fungi and inhalable dust samples were collected by stationary and personal measurements using filter samplers. Additionally, the nasal swabs from workers were taken after work-shift and microbiologically analysed. The average concentrations of inhalable dust and airborne fungi were 49 µg/m3 (SD = 91) and 299 CFU/m3 (SD = 579), respectively. Both dust and bioaerosol concentrations obtained using personal measurements were significantly higher than that measured by stationary sampling. The correlation analysis showed strong relationships between the concentrations of inhalable dust and airborne fungi (R = 0.57; p < 0.001). The fungal concentrations in swab samples from archive workers (median: 104 CFU/ml) were significantly higher than that in swabs from librarians (median: 1.4 CFU/ml). Among the airborne fungi, the widest spectrum of species was found among Penicillium and Aspergillus (including pathogenic A. fumigatus) genera. However, in samples from archives, yeast-like fungi from Sporidiobolus and Candida (including pathogenic C. albicans) genera predominated among isolated mycobiota. The results of this study revealed that airborne fungi were able to efficiently contaminate the nasal cavity of archive and library employees. The analysis of nasal swabs can be considered as an important analytical tool supporting the assessment of workers' exposure to bioaerosols. [ABSTRACT FROM AUTHOR]

Staphylococcus aureus (S. aureus) is a commensal bacterium associated with serious infections in men and animals. Recently, multidrug-resistant (MDR) strains of S. aureus especially the so-called methicillin-resistant S. aureus (MRSA), represent a serious challenge that hinders the control of infections in man and animals. This study aimed to monitor milk samples from mastitic cows and vaginal and nasal swabs from dogs for the incidence of S. aureus. In addition, the isolates' antibiogram profiles were assessed to determine the extent of MDR and MRSA existence among the recovered isolates. Out of 260 samples, 29 (11%) S. aureus isolates were recovered with the highest incidence in milk samples (15/90, 17%), followed by vaginal swabs (8/90, 9%) and nasal swabs (6/80, 7%). Identification of the isolates was confirmed by PCR amplification of 16S rRNA gene sequence. Twenty S. aureus isolates were tested against seven antibacterial agents. Surprisingly, all the twenty isolates were MRSA and three bitch vaginal isolates were MDR. The findings of this study call for more research and cooperation between authors interested in assessing the MRSA and MRD bacterial incidence in both medical and veterinary fields. The cooperation will augment the challenge of disseminating MRSA and MDR staphylococci from animals to humans and vice versa.

The post-COVID-19 recovery period is characterized by persistence of some symptoms, with immunological alterations being of great importance. Development of preventive measures to normalize mucosal immunity after a coronavirus infection determines the relevance of the current study. The aim was to study dynamics of clinical symptoms and level of secretory immunoglobulin A in individuals after a novel coronavirus infection as well as evaluate effectiveness of using IFNa-2b. Materials and methods. A study was conducted with patients aged 18 to 60 years old (n = 130), surveyed 1 to 9 months after post-infection, as well as in apparently healthy individuals lacking COVID-19 (n = 15). Previous novel coronavirus infection and post-COVID manifestations were verified based on medical documentation, complaints, anamnesis data, physical examination and questionnaires. The concentration of salivatory and nasopharyngeal mucosal sIgA was measured dynamically prior to and after administration of local therapy with IFNa-2b (gel applied intranasally twice a day for 30 days). Results. The acute period of COVID-19 was characterized by fever, anosmia, severe asthenia (fatigue and weakness), muscle and joint pain. Among the post-COVID manifestations at early period (13 months), pain in the joints and muscles (75.0%) as well as elevated body temperature (21.2%) were reliably detected, whereas in the long period (69 months) there were revealed dominance with the same frequency of shortness of breath, muscle and joint pain (75.8%, respectively). Based on examination data in healthy subjects, there was determined an arbitrary normal range of secretory IgA in saliva 6.451.81 mg/ml and nasal swabs 13.433.24 mg/ml. In the group of patients 13 months post-infection, therapy with IFNa-2b one month later resulted in significantly increased level of secretory IgA in saliva (from 1.840.28 to 5.781.96 mg/ml) and in nasal swabs (from 28.613.0 to 39.833.85 mg/ml) by more than 3- and 1.5-fold, respectively. In the group of patients without therapy was featured with stably sustained decline in sIgA level up to 9 months after COVID-19. In particular, the level of saliva sIgA ranged from 2.360.56 down to 2.160.66 mg/ml, and in nasal smears from 15.661.32 to 10.231.07 mg/ml that differed insignificantly compared to baseline level. The rate of respiratory diseases prevailed in this group (27.6% of cases), which fully lacked in the group of topically administered IFNa-2b. Conclusion. In the post-COVID period, multiple organ disorders persist and reduced sIgA level is registered. Intranasally applied IFNa-2b made possible to normalize sIgA level and prevent accumulation of respiratory infectious pathologies.

This study investigated the presence of MRSA in sheep. The study was conducted in 2022 using 100 samples, including 50 raw milk samples and 50 nasal swabs obtained from 10 flocks of sheep that were housed in various places along the North Coast area of Egypt to identify and characterize MRSA. Staphylococcus aureus was isolated and identified from the samples using conventional bacteriological techniques, while MRSA was found using a culture on oxacillin resistance screening agar basal medium (ORSAB). The recovery rate of S. aureus in the examined samples of sheep was 54 and 18 %, in raw milk samples and nasal swabs of sheep, respectively. In addition, the prevalence of confirmed MRSA strains isolated from sheep samples was 51.6 and 66.7% in milk samples and nasal swabs, respectively with total prevalence of 55.6% (20 out of 36 isolates). The antimicrobial susceptibility testing of the MRSA isolates in this study revealed varying resistance patterns. The isolates had 100% resistance to Penicillin-G and Clindamycin, 90% resistance to Linezolid, 80% resistance to Cefoxitin and 70% resistance to Erythromycin. In short, strict hygiene and biosecurity protocols should be implemented on sheep farms to avoid this from turning into a serious illness that may be deadly. According to the present inquiry, MRSA was discovered in the milk and nasal samples of sheep grown on Alexandria's North Coast that appeared to be in good health. [ABSTRACT FROM AUTHOR]

Morganella morganii (M. morganii) is a member of the genera Morganella in the Enterobacteriaceae family. We tried to better understand the prevalence and characterization of M. morganii strains in cattle. A total of 191 nasal swab samples from beef cattle in Guang'an, Yibin, and Ziyang, Sichuan province, China were collected. The presence of M. morganii in the swabs was determined by PCR. Then positive swabs were processed using bacterial isolation and identification. The M. morganii isolates were assayed for antimicrobial susceptibility and pathogenicity using a mouse model. The prevalence of M. morganii in three cities was 10.5% (20/191). Three M. morganii strains (16GA7, 17GA61.2, and 17YB9) were isolated and identified from positive swab samples. Phylogenetic analysis demonstrated that the 16S rRNA gene of M. morganii isolates could be clustered with known Genbank M. morganii strains. All three M. morganii strains were sensitive to penicillin-type and quinolone antibiotics and were resistant to some cephalosporins, carbapenems, macrolide antibiotics and polymyxin B. Lesions in mice inoculated with M. morganii included pulmonary hemorrhage, thickened alveolar walls and pulmonary inflammatory cell infiltration, although lesions varied by strain. Through research on the M. morganii in beef cattle, it was found that mice were susceptible to M. morganii isolates. To the best of our knowledge, the present study is the first to report the prevalence of M. morganii in beef cattle. [ABSTRACT FROM AUTHOR]

The virus discovered in 2019 in the city of Wuhan, China, which was later identified as SARS-CoV-2 and which spread to the level of a pandemic, put diagnostic methods to the test. Early in the pandemic, we developed a nested PCR assay for the detection of SARS-CoV-2, which we validated and applied to detect the virus in feline samples. The present study describes the application of the nested PCR test in parallel with LAMP for the detection of the virus in 427 nasopharyngeal and oropharyngeal human samples taken between October 2020 and January 2022. Of the swabs tested, there were 43 positives, accounting for 10.1% of all samples tested, with the negatives numbering 382, i.e., 89.5%, and there were 2 (0.4%) invalid ones. The nPCR results confirmed those obtained by using LAMP, with results concordant in both methods. Nasal swabs tested using nPCR confirmed the results of oropharyngeal and nasopharyngeal swab samples tested using LAMP and nPCR. The focus of the discussion is on the two techniques: the actual practical application of the laboratory-developed assays and the diagnostic value of nasal samples. The nPCR used is a reliable and sensitive technique for the detection of SARS-CoV-2 in nasopharyngeal, oropharyngeal, and nasal swab samples. However, it has some disadvantages related to the duration of the entire process, as well as a risk of contamination. Experiments were performed to demonstrate the infectivity of the virus from the positive isolates in vitro. A discrepancy was reported between direct and indirect methods of testing the virus and accounting for its ability to cause infection in vitro.

Abstract Background In dogs with sinonasal aspergillosis (SNA) the utility of PCR in the diagnosis and monitoring of the disease after treatment has not been assessed. Objectives To evaluate the presence of fungal DNA using quantitative PCR targeting Aspergillus fumigatus (Aspfum) and Aspergillus spp. (PanAsp), and PCR targeting multiple fungal species (PanFun), in samples obtained from nasal cavities of dogs with SNA, other nasal diseases and healthy dogs. Animals Sixty‐two dogs including 20 with SNA, 12 with cured SNA (of which 10 are from the SNA group), 20 dogs with Non‐SNA nasal disease, and 20 healthy dogs. Methods Prospective cross‐sectional study. Aspfum, PanAsp, and PanFun were performed on blindly collected nasal swabs obtained in anesthetized dogs. Results In SNA dogs, Aspfum and PanAsp were positive in 13/20 and 14/20 dogs. In all dogs in the 3 other groups, A. fumigatus DNA was not detected using Aspfum. PanAsp was positive in 3 non‐SNA dogs: 1 with cured SNA and 2 with Non‐SNA nasal disease. A Ct cut‐off value of 33.3 for Aspfum demonstrated 65% sensitivity and 100% specificity. A Ct cut‐off value of 34.5 for PanAsp demonstrated 70% sensitivity and 96.2% specificity. PanFun was positive in 16/20, 12/12, 19/20, and 7/20 dogs in the SNA, cured SNA, Non‐SNA, and healthy groups, respectively. Conclusion and Clinical Importance Aspfum and PanAsp on blindly collected nasal swabs can be useful for the detection of SNA at diagnosis and at cure, especially when more invasive methods are not available.

Abstract Background The Middle East Respiratory Syndrome coronavirus (MERS‐CoV) is still listed on the WHO Research and Development Blueprint of emerging pathogens. Dromedary camels remain the only known animal reservoir of the virus. The animal‐to‐animal as well as the animal‐to‐human transmission in the MERS‐CoV cycles were reported. However, many aspects of these transmission chains are not well studied. One of these directions is the potential roles of various species of arthropods in the transmission of the virus. Objectives The main goal of the current work was to study the roles of several species of arthropods in the transmission of MERS‐CoV. Methodology To achieve this goal, we identified some MERS‐CoV naturally infected dromedary camel populations. We conducted a longitudinal study among these animals for more than 2 months. This was done by repeated testing of nasal swabs biweekly from some selected animals in this population for the presence of MERS‐CoV‐RNAs by real‐time PCR. During the duration of this study, we collected several species of arthropods (Culicoides, Stomoxys, Musca domestica and some Culex species) that shared the habitat and were circulating in this farm during this longitudinal study. Results Our results showing, despite the detection of the viral RNAs in some animals throughout this study, none of the examined species of arthropods tested positive for the viral RNA. Conclusions These results are suggesting that at least the tested species of arthropods may not play roles in the transmission of MERS‐CoV. However, more large‐scale studies are required to explore any potential roles of arthropods in the transmission cycle of MERS‐CoV.

Staphylococcus aureus (S. aureus) is a commensal bacterium associated with serious infections in men and animals. Recently, multidrug-resistant (MDR) strains of S. aureus especially the so-called methicillin-resistant S. aureus (MRSA), represent a serious challenge that hinders the control of infections in man and animals. This study aimed to monitor milk samples from mastitic cows and vaginal and nasal swabs from dogs for the incidence of S. aureus. In addition, the isolates' antibiogram profiles were assessed to determine the extent of MDR and MRSA existence among the recovered isolates. Out of 260 samples, 29 (11%) S. aureus isolates were recovered with the highest incidence in milk samples (15/90, 17%), followed by vaginal swabs (8/90, 9%) and nasal swabs (6/80, 7%). Identification of the isolates was confirmed by PCR amplification of 16S rRNA gene sequence. Twenty S. aureus isolates were tested against seven antibacterial agents. Surprisingly, all the twenty isolates were MRSA and three bitch vaginal isolates were MDR. The findings of this study call for more research and cooperation between authors interested in assessing the MRSA and MRD bacterial incidence in both medical and veterinary fields. The cooperation will augment the challenge of disseminating MRSA and MDR staphylococci from animals to humans and vice versa. [ABSTRACT FROM AUTHOR]

Compared to nasopharyngeal swabs (NPS), there has been insufficient evaluation of the diagnostic performance of nasal swabs (NS) for the detection of severe acute respiratory coronavirus 2 (SARS-CoV-2) in the nucleic acid amplification test (NAAT) and quantitative SARS-CoV-2 antigen test (QAT). We prospectively compared healthcare worker-collected and flocked NS within nine days after symptom onset to paired NPS to detect SARS-CoV-2 in NAAT and QAT on the fully automated Lumipulse system. The agreement between sample types was evaluated, and cycle threshold (Ct) values and antigen levels were used as surrogate viral load measures. Sixty sets of NPS and NS samples were collected from 40 patients with COVID-19. The overall agreements between NAAT and QAT samples were 76.7% and 65.0%, respectively. In NAAT, the Ct value of NS was significantly higher, 5.9, than that of NPS. Thirty-nine (95.1%) NS tested positive in 41 positive-paired NPS with Ct ≤ 30. The negative correlation was observed between antigen levels of NS in QAT and Ct values of NS in NAAT (r = −0.88). In QAT, the antigen level of NS was significantly lower than that of NPS. Thirty-six (90.0%) NS tested positive in 40 positive-paired NPS with antigen levels >100 pg/mL, which were collected significantly earlier than those with antigen levels ≤100 pg/mL. In NAAT and QAT, NS had limited performance in detecting SARS-CoV-2 compared to NPS. However, NS may be helpful for patients with COVID-19 with high viral loads or those in the early stages of the illness. [ABSTRACT FROM AUTHOR]

Staphylococcus aureus is one of the common causes of Healthcare-associated infection. Staphylococcus colonizes the anterior nares of the nose and tends to disseminate and secondarily colonize several other body sites including the skin and the gut. Colonized hospital personnel may be an important factor in dissemination. Staphylococcus aureus to patients and vice-versa. Mupirocin is an excellent topical anti-staphylococcal antimicrobial agent used for eradicating nasal carriage. Resistance to Mupirocin is a threat for future use of this drug in eliminating nasal carriage of Staphylococcus aureus. Thus, this study was conducted to determine the rate of Mupirocin resistance among Staphylococcus aureus isolated from nasal swabs of Health care workers (HCWs ) of Operation Theatres (OTs) and Intensive Care Units (ICUs). A single nasal swab was collected from both the anterior nares of participating health care workers of ICU and OT once at the end of their shift. Antibiotic susceptibility testing of Staphylococcus aureus to various antibiotics was done by Kirby-Bauer disk diffusion method using CLSI guidelines. High and low-level Mupirocin resistance was determined. Among 282 nasal swabs collected, Staphylococcus aureus was isolated in 62 samples. Of Staphylococcus aureus 19 came out to be Methicillin-resistant (MRSA) and the remaining 43 Methicillin sensitive (MSSA). Mupirocin resistance was seen in 3 MRSA strains and 1 MSSA strain. Thus, overall 4/62 (6.5%) strains were MupR strains. Mupirocin is the most effective antibiotic used against colonization of Staphylococcus aureus in anterior nares. Resistance to this antibiotic is thus an alarm as well as a matter of great concern. Necessary steps, policies and guidelines need to be framed to stop the spread of this resistance.

Background: In resource-poor countries, antigen-based rapid tests (Ag-RDTs) performed at primary healthcare and community settings improved access to SARS-CoV-2 diagnostics. However, the technical skills and biosafety requirements inherent to nasopharyngeal and oropharyngeal (OP) specimens limit the scale-up of SARS-CoV-2 testing. The collection of nasal-swabs is programmatically viable, but its performance has not been evaluated in resource-poor settings. Methods: We first evaluated the performance of SteriPack self-collected nasal swabs for the detection of SARS-CoV-2 by real-time PCR in 1498 consecutively enrolled patients with suspected infection. Next, we evaluated the clinical performance of three nasal swab-based Ag-RDTs against real-time PCR on OP specimens. Results: The sensitivity of nasal swabs was 80.6% [95% CI: 75.3–85.2%] compared to OP specimens. There was a good correlation (r = 0.58; p < 0.0001) between Ct values of 213 positive cases obtained using nasal and OP swabs. Our findings show sensitivities of 79.7% [95% CI: 73.3–85.1%] for Panbio COVID-19 Ag-RDT, 59.6% [95% CI: 55.2–63.8%] for COVIOS Ag-RDT, and 78.0% [95% CI: 73.5–82.0%] for the LumiraDx SARS-CoV-2 Ag-RDT. Conclusions: In our setting, the COVIOS Ag-RDT did not meet WHO requirements. Nasal swab-based Ag-RDTs for SARS-CoV-2 detection constitute a viable and accurate diagnostic option in resource-poor settings. [ABSTRACT FROM AUTHOR]

Abstract 3-dimensional (3D) printing technology provides a solution to meet the high demand for producing adult nasal swabs. A smaller, more flexible nasopharyngeal swab needs to be developed for children and infants suspected of having coronavirus. The information shared here presents a novel 3D-printed pediatric swab for the purpose of collecting upper respiratory clinical specimens.

Little information is presently available regarding the frequency of the silent shedders of respiratory viruses in healthy sport horses and their impact on environmental contamination. Therefore, the aim of this study was to investigate the detection frequency of selected respiratory pathogens in nasal secretions and environmental stall samples of sport horses attending a multi-week equestrian event during the summer months. Six out of fifteen tents were randomly selected for the study with approximately 20 horse/stall pairs being sampled on a weekly basis. Following weekly collection for a total of 11 weeks, all samples were tested for the presence of common respiratory pathogens (EIV, EHV-1, EHV-4, ERAV, ERBV, and Streptococcus equi ss equi (S. equi)) using qPCR. A total of 19/682 nasal swabs (2.8%) and 28/1288 environmental stall sponges (2.2%) tested qPCR-positive for common respiratory pathogens. ERBV was the most common respiratory virus (17 nasal swabs, 28 stall sponges) detected, followed by EHV-4 (1 nasal swab) and S. equi (1 nasal swab). EIV, EHV-1, EHV-4 and ERAV were not detected in any of the study horses or stalls. Only one horse and one stall tested qPCR-positive for ERBV on two consecutive weeks. All the other qPCR-positive sample results were related to individual time points. Furthermore, only one horse/stall pair tested qPCR-positive for ERBV at a single time point. The study results showed that in a selected population of sport horses attending a multi-week equestrian event in the summer, the frequency of the shedding of respiratory viruses was low and primarily restricted to ERBV with little evidence of active transmission and environmental contamination.

COVID-19 is a life-threatening multisistemic infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Infection control relies on timely identification and isolation of infected people who can alberg the virus for up to 14 days, providing important opportunities for undetected transmission. This note describes the application of rRT-PCR test for simpler, faster and less invasive monitoring of SARS-CoV-2 infection using pooling strategy of samples. Seventeen positive patients were provided with sterile dry swabs and asked to self-collected 2 nasal specimens (#NS1 and #NS2). The #NS1 was individually placed in a single tube and the #NS2 was placed in another tube together with 19 NSs collected from 19 negative patients. Both tubes were then tested with conventional molecular rRT-PCR and the strength of pooling nasal testing was compared with the molecular test performed on the single NS of each positive patient. The pooling strategy detected SARS-CoV-2 RNA to a similar extent to the single test, even when Ct value is on average high (Ct 37-38), confirming that test sensibility is not substantially affected even if the pool contains only one low viral load positive sample. Furthermore, the pooling strategy have benefits for SARS-CoV-2 routinary monitoring of groups in regions with a low SARS-CoV-2 prevalence. [ABSTRACT FROM AUTHOR]

Background: In dogs with sinonasal aspergillosis (SNA) the utility of PCR in the diagnosis and monitoring of the disease after treatment has not been assessed. Objectives: To evaluate the presence of fungal DNA using quantitative PCR targeting Aspergillus fumigatus (Aspfum) and Aspergillus spp. (PanAsp), and PCR targeting multiple fungal species (PanFun), in samples obtained from nasal cavities of dogs with SNA, other nasal diseases and healthy dogs. Animals: Sixty‐two dogs including 20 with SNA, 12 with cured SNA (of which 10 are from the SNA group), 20 dogs with Non‐SNA nasal disease, and 20 healthy dogs. Methods: Prospective cross‐sectional study. Aspfum, PanAsp, and PanFun were performed on blindly collected nasal swabs obtained in anesthetized dogs. Results: In SNA dogs, Aspfum and PanAsp were positive in 13/20 and 14/20 dogs. In all dogs in the 3 other groups, A. fumigatus DNA was not detected using Aspfum. PanAsp was positive in 3 non‐SNA dogs: 1 with cured SNA and 2 with Non‐SNA nasal disease. A Ct cut‐off value of 33.3 for Aspfum demonstrated 65% sensitivity and 100% specificity. A Ct cut‐off value of 34.5 for PanAsp demonstrated 70% sensitivity and 96.2% specificity. PanFun was positive in 16/20, 12/12, 19/20, and 7/20 dogs in the SNA, cured SNA, Non‐SNA, and healthy groups, respectively. Conclusion and Clinical Importance: Aspfum and PanAsp on blindly collected nasal swabs can be useful for the detection of SNA at diagnosis and at cure, especially when more invasive methods are not available. [ABSTRACT FROM AUTHOR]

Simple Summary: Due to concerns in public health and its negative impact on the pig industry the need for Influenza A virus (IAV) surveillance is rising. The gold standard procedure for detecting IAV is to sample acutely diseased pigs. Endemic infections with unspecific clinical signs and low disease prevalence need new approaches. Our study aimed to evaluate a standardized sampling procedure for the detection of IAV in epidemically and endemically infected farms. We performed a cross-sectional study in 131 farms investigating three different age groups per farm in 12 European countries. The results of our investigation indicate that 10 nasal swabs each in suckling piglets, weaners and middle of nursery is a valuable tool for influenza detection and identification of subtypes. However, for farms with a lower prevalence than 15% it is advisable to either increase the number of nasal swabs in each age group or to use group sampling methods. Interestingly, different subtypes were found in different age groups. Thus, our study underlines that sampling of different age groups is mandatory to obtain a comprehensive overview on all circulating variants on farm. In addition, our results highlight that sampling strategies should also consider piglets without obvious clinical signs for IAV infection. Swine influenza A virus (swIAV), which plays a major role in the porcine respiratory disease complex (PRDC), is eliminated from the respiratory tract within 7–9 days after infection. Therefore, diagnosis is complicated in endemically infected swine herds presenting no obvious clinical signs. This study aimed to investigate the right time point for sampling to detect swIAV. A cross-sectional study was performed in 131 farms from 12 European countries. The sampling protocol included suckling piglets, weaners, and nursery pigs. In each age group, 10 nasal swabs were collected and further examined in pools of 5 for swIAV by Matrix rRT-PCR, followed by a multiplex RT-PCR to determine the influenza subtype. SwIAV was detected in 284 (37.9%) of the samples and on 103 (78.6%) farms. Despite the highest number of animals with clinical signs being found in the nursery, the weaners were significantly more often virus-positive compared to nursery pigs (p = 0.048). Overall, the swIAV detection rate did not significantly differ between diseased or non-diseased suckling and nursery piglets, respectively; however, diseased weaners had significantly more positive pools than the non-diseased animals. Interestingly, in 9 farms, different subtypes were detected in different age groups. Our findings indicate that to detect all circulating swIAV subtypes on a farm, different age groups should be sampled. Additionally, the sampling strategy should also aim to include non-diseased animals, especially in the suckling period. [ABSTRACT FROM AUTHOR]

Background: The Middle East Respiratory Syndrome coronavirus (MERS‐CoV) is still listed on the WHO Research and Development Blueprint of emerging pathogens. Dromedary camels remain the only known animal reservoir of the virus. The animal‐to‐animal as well as the animal‐to‐human transmission in the MERS‐CoV cycles were reported. However, many aspects of these transmission chains are not well studied. One of these directions is the potential roles of various species of arthropods in the transmission of the virus. Objectives: The main goal of the current work was to study the roles of several species of arthropods in the transmission of MERS‐CoV. Methodology: To achieve this goal, we identified some MERS‐CoV naturally infected dromedary camel populations. We conducted a longitudinal study among these animals for more than 2 months. This was done by repeated testing of nasal swabs biweekly from some selected animals in this population for the presence of MERS‐CoV‐RNAs by real‐time PCR. During the duration of this study, we collected several species of arthropods (Culicoides, Stomoxys, Musca domestica and some Culex species) that shared the habitat and were circulating in this farm during this longitudinal study. Results: Our results showing, despite the detection of the viral RNAs in some animals throughout this study, none of the examined species of arthropods tested positive for the viral RNA. Conclusions: These results are suggesting that at least the tested species of arthropods may not play roles in the transmission of MERS‐CoV. However, more large‐scale studies are required to explore any potential roles of arthropods in the transmission cycle of MERS‐CoV. [ABSTRACT FROM AUTHOR]

COVID-19 is a life-threatening multisistemic infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Infection control relies on timely identification and isolation of infected people who can alberg the virus for up to 14 days, providing important opportunities for undetected transmission. This note describes the application of rRT-PCR test for simpler, faster and less invasive monitoring of SARS-CoV-2 infection using pooling strategy of samples. Seventeen positive patients were provided with sterile dry swabs and asked to self-collected 2 nasal specimens (#NS1 and #NS2). The #NS1 was individually placed in a single tube and the #NS2 was placed in another tube together with 19 NSs collected from 19 negative patients. Both tubes were then tested with conventional molecular rRT-PCR and the strength of pooling nasal testing was compared with the molecular test performed on the single NS of each positive patient. The pooling strategy detected SARS-CoV-2 RNA to a similar extent to the single test, even when Ct value is on average high (Ct 37–38), confirming that test sensibility is not substantially affected even if the pool contains only one low viral load positive sample. Furthermore, the pooling strategy have benefits for SARS-CoV-2 routinary monitoring of groups in regions with a low SARS-CoV-2 prevalence.

Abstract Objective The Middle East respiratory syndrome coronavirus (MERS-CoV) is one of the zoonotic coronaviruses [Hemida Peer J 7:e7556, 2019; Hemida et al. One Health 8:100102, 2019]. The dromedary camels remained the only known animal reservoir for this virus. Several aspects of the transmission cycle of the virus between animals, including arthropod-borne infection, is still largely unknown. The main objective of the current work was to study the possibility of MERS-CoV transmission through some arthropod vectors, particularly the hard ticks. To achieve this objective, we identified a positive MERS-CoV dromedary camel herd using the commercial available real-time PCR kits. We collected some arthropods, particularly the ticks from these positive animals as well as from the animal habitats. We tested these arthropods for the presence of MERS-CoV viral RNAs. Results Our results showing the absence of any detectable MERS-CoV-RNAs in these arthropods despite these animals were actively shedding the virus in their nasal secretions. Our results are confirming for the first the failure of detection of the MERS-CoV in ticks infesting dromedary camels. Failure of the detection of MERS-CoV in ticks infesting positive naturally infected MERS-CoV camels is strongly suggesting that ticks do not play roles in the transmission of the virus among the animals and close contact humans.

Equine adenovirus 1 (EAdV-1) can cause upper respiratory disease in horses and has been reported worldwide. In this study, and for the first time in Korea, the prevalence of EAdV-1 in equine nasal swabs was investigated using a PCR to identify potential risk factors and examine the genetic diversity of its DNA sequences by a comparison with foreign strains. Nasal swabs collected from 359 horses reared at Korea Racing Authority facilities were tested using an EAdV-1 hexon-specific PCR and the associations between EAdV-1 infection and sex, age, region, breed, and activity were analyzed. Five samples (1.4%, 5/359) tested positive for EAdV-1; however, no statistically significant differences were observed with respect to any variable. Among the five EAdV-1-positive horses, a co-infection with equine influenza, equine herpesvirus 1 and 4, or Streptococcus equi was not detected; however, clinical respiratory signs were observed in one. Phylogenetic analyses based on partial EAdV-1 hexon gene sequences revealed that the Korean EAdV-1 isolates shared approximately 98.8–100% similarity among each other and with foreign strains. Three Korean isolates shared high similarity with strains from Australia and India and the remaining two isolates were separate in phylogenetic analyses. These findings highlight the molecular prevalence and genetic diversity of EAdV-1 in horses in Korea. [ABSTRACT FROM AUTHOR]

Background Nasopharyngeal (NP) swabs are the standard for SARS-CoV-2 diagnosis. If less invasive alternatives to NP swabs (eg, oropharyngeal [OP] or nasal swabs [NS]) are comparably sensitive, the use of these techniques may be preferable in terms of comfort, convenience, and safety. Methods This study compared the detection of SARS-CoV-2 in swab samples collected on the same day among participants with at least one positive PCR test. Results Overall, 755 participants had at least one set of paired swabs. Concordance between NP and other swab types was 75% (NS), 72% (OP), 54% (rectal swabs [RS]), and 78% (NS/OP combined). Kappa values were moderate for the NS, OP, and NS/OP comparisons (0.50, 0.45, and 0.54, respectively). Highest sensitivity relative to NP (0.87) was observed with a combination of NS/OP tests (positive if either NS or OP was positive). Sensitivity of the non-NP swab types was highest in the first week postsymptom onset and decreased thereafter. Similarly, virus RNA quantity was highest in the NP swabs as compared with NS, OP, and RS within two weeks postsymptom onset. OP and NS performance decreased as virus RNA quantity decreased. No differences were noted between NS specimens collected at home or in clinic. Conclusions NP swabs detected more SARS-CoV-2 cases than non-NP swabs, and the sensitivity of the non-NP swabs decreased with time postsymptom onset. While other swabs may be simpler to collect, NP swabs present the best chance of detecting SARS-CoV-2 RNA, which is essential for clinical care as well as genomic surveillance. [ABSTRACT FROM AUTHOR]

Community-acquired pneumonia (CAP) in children is still one of the leading causes of morbidity and mortality, especially in developing countries. The World Health Organization (WHO) has reported that pneumonia accounts for 15% of all deaths of children under 5 years old. The aim of the present study was to find out the predominance of microorganisms in the respiratory tract in children. 334 strains of microorganisms were isolated: Gram-positive – 293 strains, Gram-negative – 41. From the pharynx 183 strains were isolated, from the nose – 94, from sputum – 57. Among Gram-positive microorganisms the following were isolated: Staphylococcus aureus 44 strains of microorganisms, S. epidermidis – 75, Group A β-hemolytic streptococci – 39, viridans streptococci – 55, Streptococcus pneumoniae – 34, Enterococcus faecalis – 2, Candida spp. – 38, Corynebacterium pseudodiphthericum – 6. Among Gram-negative microorganisms the following were isolated: Escherichia coli 4 strains of microorganisms, Klebsiella pneumoniae – 13, Pseudomonas aeruginosa – 6, Haemophilus influenzae – 11, Enterobacter cloacae – 7. Children were divided by age and diagnosis into four groups: I group – children with acute bronchitis (0–5 years of age), II group – children with acute bronchitis (5–18 years of age), III group – children with CAP (0–5 years of age), IV group – children with CAP (5–18 years of age). Materials used in the research – nasal swabs, throat swabs and sputum. Microorganisms were isolated and identified using standard microbiological methods. S. aureus was the predominant microorganism isolate from the pharynx in children with bronchitis (0–5 years). Group A β-hemolytic streptococci were isolated most often from the pharynx in children with bronchitis older than 5 years and in children with CAP less than 5 years of age. S. pneumoniae was most often isolated from the pharynx in children older than 5 years of age with CAP. S. aureus was the main microorganism, isolated from the nose in children with bronchitis in all age groups; in patients with CAP it was the predominant microorganism in children older than 5 years of age. S. aureus was the predominant microorganism, isolated from sputum in children with bronchitis older than 5 years. S. pneumoniae was the predominant microorganism, isolated from sputum in children with CAP older than 5 years. The research showed that S. pneumoniae is still one of the main pathogens that cause CAP in school aged children.

Staphylococcus aureus is one of the common causes of Healthcare-associated infection. Staphylococcus colonizes the anterior nares of the nose and tends to disseminate and secondarily colonize several other body sites including the skin and the gut. Colonized hospital personnel may be an important factor in dissemination. Staphylococcus aureus to patients and vice-versa. Mupirocin is an excellent topical anti-staphylococcal antimicrobial agent used for eradicating nasal carriage. Resistance to Mupirocin is a threat for future use of this drug in eliminating nasal carriage of Staphylococcus aureus. Thus, this study was conducted to determine the rate of Mupirocin resistance among Staphylococcus aureus isolated from nasal swabs of Health care workers (HCWs) of Operation Theatres (OTs) and Intensive Care Units (ICUs). A single nasal swab was collected from both the anterior nares of participating health care workers of ICU and OT once at the end of their shift. Antibiotic susceptibility testing of Staphylococcus aureus to various antibiotics was done by Kirby-Bauer disk diffusion method using CLSI guidelines. High and low-level Mupirocin resistance was determined. Among 282 nasal swabs collected, Staphylococcus aureus was isolated in 62 samples. Of Staphylococcus aureus 19 came out to be Methicillin-resistant (MRSA) and the remaining 43 Methicillin sensitive (MSSA). Mupirocin resistance was seen in 3 MRSA strains and 1 MSSA strain. Thus, overall 4/62 (6.5%) strains were MupR strains. Mupirocin is the most effective antibiotic used against colonization of Staphylococcus aureus in anterior nares. Resistance to this antibiotic is thus an alarm as well as a matter of great concern. Necessary steps, policies and guidelines need to be framed to stop the spread of this resistance. [ABSTRACT FROM AUTHOR]

The emergence of SARS-CoV-2 variants complicates efforts to control the COVID-19 pandemic. Increasing genomic surveillance of SARS-CoV-2 is imperative for early detection of emerging variants, to trace the movement of variants, and to monitor effectiveness of countermeasures. Additionally, determining the amount of viable virus present in clinical samples is helpful to better understand the impact these variants have on viral shedding. In this study, we analyzed nasal swab samples collected between March 2020 and early November 2021 from a cohort of United States (U.S.) military personnel and healthcare system beneficiaries stationed worldwide as a part of the Defense Health Agency's (DHA) Global Emerging Infections Surveillance (GEIS) program. SARS-CoV-2 quantitative real time reverse-transcription PCR (qRT-PCR) positive samples were characterized by next-generation sequencing and a subset was analyzed for isolation and quantification of viable virus. Not surprisingly, we found that the Delta variant is the predominant strain circulating among U.S. military personnel beginning in July 2021 and primarily represents cases of vaccine breakthrough infections (VBIs). Among VBIs, we found a 50-fold increase in viable virus in nasal swab samples from Delta variant cases when compared to cases involving other variants. Notably, we found a 40-fold increase in viable virus in nasal swab samples from VBIs involving Delta as compared to unvaccinated personnel infected with other variants prior to the availability of approved vaccines. This study provides important insight about the genomic and virological characterization of SARS-CoV-2 isolates from a unique study population with a global presence.

Background: The dynamics of SARS-CoV-2 alpha variant shedding and immune responses at the nasal mucosa remain poorly characterised. Methods: We measured infectious viral release, antibodies and cytokines in 426 PCR+ nasopharyngeal swabs from individuals harboring non-alpha or alpha variants. Findings: With both lineages, viral titers were variable, ranging from 0 to >106 infectious units. Rapid antigenic diagnostic tests were positive in 94% of samples with infectious virus. 68 % of individuals carried infectious virus within two days after onset of symptoms. This proportion decreased overtime. Viable virus was detected up to 14 days. Samples containing anti-spike IgG or IgA did not generally harbor infectious virus. Ct values were slightly but not significantly lower with alpha. This variant was characterized by a fast decrease of infectivity overtime and a marked release of 13 cytokines (including IFN-b, IP-10 and IL-10). Interpretation: The alpha variant displays modified viral decay and cytokine profiles at the nasopharyngeal mucosae during symptomatic infection. Funding: This retrospective study has been funded by Institut Pasteur, ANRS, Vaccine Research Institute, Labex IBEID, ANR/FRM and IDISCOVR, Fondation pour la Recherche Médicale.

Background: Testing for SARS-CoV-2 is essential to provide early COVID-19 treatment for people at high risk of severe illness and to limit the spread of infection in society. Proper upper respiratory specimen collection is the most critical step in the diagnosis of the SARS-CoV-2 virus in public settings, and throat swabs were the preferred specimens used for mass testing in many countries during the COVID-19 pandemic. However, there is still a discussion about whether throat swabs have a high enough sensitivity for SARS-CoV-2 diagnostic testing, as previous studies have reported a large variability in the sensitivity from 52% to 100%. Many previous studies exploring the diagnostic accuracy of throat swabs lack a detailed description of the sampling technique, which makes it difficult to compare the different diagnostic accuracy results. Some studies perform a throat swab by only collecting specimens from the posterior oropharyngeal wall, while others also include a swab of the palatine tonsils for SARS-CoV-2 testing. However, studies suggest that the palatine tonsils could have a tissue tropism for SARS-CoV-2 that may improve the SARS-CoV-2 detection during sampling. This may explain the variation of sensitivity reported, but no clinical studies have yet explored the differences in sensitivity and patient discomfort whether the palatine tonsils are included during the throat swab or not., Objective: The objective of this study is to examine the sensitivity and patient discomfort of a throat swab including the palatine tonsils compared to only swabbing the posterior oropharyngeal wall in molecular testing for SARS-CoV-2., Methods: We will conduct a randomized controlled study to compare the molecular detection rate of SARS-CoV-2 by a throat swab performed from the posterior oropharyngeal wall and the palatine tonsils (intervention group) or the posterior oropharyngeal wall only (control group). Participants will be randomized in a 1:1 ratio. All participants fill out a baseline questionnaire upon enrollment in the trial, examining their reason for being tested, symptoms, and previous tonsillectomy. A follow-up questionnaire will be sent to participants to explore the development of symptoms after testing., Results: A total of 2315 participants were enrolled in this study between November 10, 2022, and December 22, 2022. The results from the follow-up questionnaire are expected to be completed at the beginning of 2024., Conclusions: This randomized clinical trial will provide us with information about whether throat swabs including specimens from the palatine tonsils will improve the diagnostic sensitivity for SARS-CoV-2 molecular detection. These results can, therefore, be used to improve future testing recommendations and provide additional information about tissue tropism for SARS-CoV-2., Trial Registration: ClinicalTrials.gov NCT05611203; https://clinicaltrials.gov/study/NCT05611203., International Registered Report Identifier (irrid): DERR1-10.2196/47446., (©Benedikte Hartvigsen, Kathrine Kronberg Jakobsen, Thomas Benfield, Niels Tobias Gredal, Annette Kjær Ersbøll, Mathias Waldemar Grønlund, Henning Bundgaard, Mikkel Porsborg Andersen, Nina Steenhard, Christian von Buchwald, Tobias Todsen. Originally published in JMIR Research Protocols (https://www.researchprotocols.org), 12.06.2024.)

Cryptococcus has gained medical importance over the last decade, as it is an emerging pathogen among immunocompetent individuals. There are no epidemiological data on the prevalence of this fungus in donkeys. The current research was conducted to investigate the possible role of the Egyptian donkeys in the epidemiology of such pathogen. Bacteriological analysis of nasal swabs of 52 diseased and healthy donkeys at different localities in Egypt revealed that the overall occurrence of Cryptococcus spp. was 11.5%. The highest proportion was in El-Fayoum Governorate (25). Phenotypic identification of Cryptococcus indicated that 13.2 % and 7.1% among healthy and diseased donkeys were positive for this pathogen, respectively. The study of the potential risk factors associated with Cryptococcus colonization in the donkeys did not show any statistically significant differences. Molecular serotyping of 6 identified Cryptococcus spp. evidenced C. gattii in the nasal passages of 4 healthy donkeys (7.7%); while the other 2 C. neoformans serotype A (3.8%) isolates identified in healthy and diseased donkeys. Four C. gattii and C. neoformans isolates demonstrated higher laccase (LAC1) genes among the identified virulence factors. While capsular associated protein (CAP59) gene identified alone or associated with LAC1 gene in the other 2 C. gattii isolates. This study underlines a potential association of those fungi with human disease in Egypt. In order to strengthen existing therapeutic and control approaches, further analyses of the main risk factors and the other virulence of these pathogens should be further considered. [ABSTRACT FROM AUTHOR]

Middle East respiratory syndrome coronavirus (MERS‐CoV) is one of the recently identified zoonotic coronaviruses. The one‐hump camels are believed to play important roles in the evolution and transmission of the virus. The animal‐to‐animal, as well as the animal‐to‐human transmission in the context of MERS‐CoV infection, were reported. The camels shed the virus in some of their secretions, especially the nasal tract. However, there are many aspects of the transmission cycle of the virus from animals to humans that are still not fully understood. Rodents played important roles in the transmission of many pathogens, including viruses and bacteria. They have been implicated in the evolution of many human coronaviruses, especially HCoV‐OC43 and HCoV‐HKU1. However, the role of rodents in the transmission of MERS‐CoV still requires more exploration. To achieve this goal, we identified MERS‐CoV that naturally infected dromedary camel by molecular surveillance. We captured 15 of the common rodents (rats, mice, and jerboa) sharing the habitat with these animals. We collected both oral and rectal swabs from these animals and then tested them by the commercial MERS‐CoV real‐time‐PCR kits using two targets. Despite the detection of the viral shedding in the nasal swabs of some of the dromedary camels, none of the rodents tested positive for the virus during the tenure of this study. We concluded that these species of rodents did not harbor the virus and are most unlikely to contribute to the transmission of the MERS‐CoV. However, further large‐scale studies are required to confirm the potential roles of rodents in the context of the MERS‐CoV transmission cycle, if any. [ABSTRACT FROM AUTHOR]

3-dimensional (3D) printing technology provides a solution to meet the high demand for producing adult nasal swabs. A smaller, more flexible nasopharyngeal swab needs to be developed for children and infants suspected of having coronavirus. The information shared here presents a novel 3D-printed pediatric swab for the purpose of collecting upper respiratory clinical specimens. [ABSTRACT FROM AUTHOR]

Background: In resource-poor countries, antigen-based rapid tests (Ag-RDTs) performed at primary healthcare and community settings improved access to SARS-CoV-2 diagnostics. However, the technical skills and biosafety requirements inherent to nasopharyngeal and oropharyngeal (OP) specimens limit the scale-up of SARS-CoV-2 testing. The collection of nasal-swabs is programmatically viable, but its performance has not been evaluated in resource-poor settings. Methods: We first evaluated the performance of SteriPack self-collected nasal swabs for the detection of SARS-CoV-2 by real-time PCR in 1498 consecutively enrolled patients with suspected infection. Next, we evaluated the clinical performance of three nasal swab-based Ag-RDTs against real-time PCR on OP specimens. Results: The sensitivity of nasal swabs was 80.6% [95% CI: 75.3–85.2%] compared to OP specimens. There was a good correlation (r = 0.58; p < 0.0001) between Ct values of 213 positive cases obtained using nasal and OP swabs. Our findings show sensitivities of 79.7% [95% CI: 73.3–85.1%] for Panbio COVID-19 Ag-RDT, 59.6% [95% CI: 55.2–63.8%] for COVIOS Ag-RDT, and 78.0% [95% CI: 73.5–82.0%] for the LumiraDx SARS-CoV-2 Ag-RDT. Conclusions: In our setting, the COVIOS Ag-RDT did not meet WHO requirements. Nasal swab-based Ag-RDTs for SARS-CoV-2 detection constitute a viable and accurate diagnostic option in resource-poor settings.

Objective: The Middle East respiratory syndrome coronavirus (MERS-CoV) is one of the zoonotic coronaviruses [Hemida Peer J 7:e7556, 2019; Hemida et al. One Health 8:100102, 2019]. The dromedary camels remained the only known animal reservoir for this virus. Several aspects of the transmission cycle of the virus between animals, including arthropod-borne infection, is still largely unknown. The main objective of the current work was to study the possibility of MERS-CoV transmission through some arthropod vectors, particularly the hard ticks. To achieve this objective, we identified a positive MERS-CoV dromedary camel herd using the commercial available real-time PCR kits. We collected some arthropods, particularly the ticks from these positive animals as well as from the animal habitats. We tested these arthropods for the presence of MERS-CoV viral RNAs. Results: Our results showing the absence of any detectable MERS-CoV-RNAs in these arthropods despite these animals were actively shedding the virus in their nasal secretions. Our results are confirming for the first the failure of detection of the MERS-CoV in ticks infesting dromedary camels. Failure of the detection of MERS-CoV in ticks infesting positive naturally infected MERS-CoV camels is strongly suggesting that ticks do not play roles in the transmission of the virus among the animals and close contact humans. [ABSTRACT FROM AUTHOR]

Swine influenza A virus (swIAV), which plays a major role in the porcine respiratory disease complex (PRDC), is eliminated from the respiratory tract within 7–9 days after infection. Therefore, diagnosis is complicated in endemically infected swine herds presenting no obvious clinical signs. This study aimed to investigate the right time point for sampling to detect swIAV. A cross-sectional study was performed in 131 farms from 12 European countries. The sampling protocol included suckling piglets, weaners, and nursery pigs. In each age group, 10 nasal swabs were collected and further examined in pools of 5 for swIAV by Matrix rRT-PCR, followed by a multiplex RT-PCR to determine the influenza subtype. SwIAV was detected in 284 (37.9%) of the samples and on 103 (78.6%) farms. Despite the highest number of animals with clinical signs being found in the nursery, the weaners were significantly more often virus-positive compared to nursery pigs (p = 0.048). Overall, the swIAV detection rate did not significantly differ between diseased or non-diseased suckling and nursery piglets, respectively; however, diseased weaners had significantly more positive pools than the non-diseased animals. Interestingly, in 9 farms, different subtypes were detected in different age groups. Our findings indicate that to detect all circulating swIAV subtypes on a farm, different age groups should be sampled. Additionally, the sampling strategy should also aim to include non-diseased animals, especially in the suckling period.

Introduction: Severe acute respiratory syndrome coronavirus-2 (SARS CoV 2) virus, a causative agent of COVID-19 has led to universal pandemic. During this pandemic there has been an acute shortage of good quality Viral Transport Medium (VTM) because of increase in number of infected people worldwide. It is also difficult to maintain the transport and storing conditions in line with the guidelines in pandemics. Aim: To assess the feasibility of Oropharyngeal Swab (OP)/ Nasal swabs in 0.9% normal saline in place of VTM and to analyse the effect of temperature on nucleic acid detection by rRT PCR on saline samples stored at 4ºC, ambient and at higher temperature (37ºC). Materials and Methods: The present study was an observational analytical study which included 94 positive and 5 negative samples. Patients' nasal or OP samples were collected as dry swabs and in VTM. Normal saline was added once the samples were received in the laboratory. PCR was done with saline and VTM samples both on day 1. Samples were aliquotted in 3 sets and one set was kept at 4º-8º C and other two at 25ºC and 37ºC, respectively. All positive samples were further tested on day 3, day 4 and day 6. Results were analysed and compared. Results: Samples in normal saline showed very good sensitivity at all temperatures (4º-8ºC, 25ºC and 37ºC) till day 6. Both the swab samples (in saline and in VTM) showed nearly 100% agreement in rRT-PCR results. Ct value variation was also ≤±2. Conclusion: Looking into the cost and logistics issues especially during pandemics, saline is a good and cheaper alternative to VTM and with its use, testing capacity can be expanded.

Introduction: Severe acute respiratory syndrome coronavirus-2 (SARS CoV 2) virus, a causative agent of COVID-19 has led to universal pandemic. During this pandemic there has been an acute shortage of good quality Viral Transport Medium (VTM) because of increase in number of infected people worldwide. It is also difficult to maintain the transport and storing conditions in line with the guidelines in pandemics. Aim: To assess the feasibility of Oropharyngeal Swab (OP)/Nasal swabs in 0.9% normal saline in place of VTM and to analyse the effect of temperature on nucleic acid detection by rRT PCR on saline samples stored at 4°C, ambient and at higher temperature (37°C). Materials and Methods: The present study was an observational analytical study which included 94 positive and 5 negative samples. Patients' nasal or OP samples were collected as dry swabs and in VTM. Normal saline was added once the samples were received in the laboratory. PCR was done with saline and VTM samples both on day 1. Samples were aliquotted in 3 sets and one set was kept at 4°-8° C and other two at 25°C and 37°C, respectively. All positive samples were further tested on day 3, day 4 and day 6. Results were analysed and compared. Results: Samples in normal saline showed very good sensitivity at all temperatures (4°-8°C, 25°C and 37°C) till day 6. Both the swab samples (in saline and in VTM) showed nearly 100% agreement in rRT-PCR results. Ct value variation was also =±2. Conclusion: Looking into the cost and logistics issues especially during pandemics, saline is a good and cheaper alternative to VTM and with its use, testing capacity can be expanded. [ABSTRACT FROM AUTHOR]

Purpose: Endoscopic endonasal skull base surgery (EESBS) is a clean-contaminated procedure. Guidelines regarding the antibiotic prophylaxis in EESBS have not been developed yet, and today, there are no universally accepted protocols. In this article, we investigated the efficacy of our new ultra-short antibiotic prophylaxis protocol for EESBS guided by the cultural results of preoperative microbiological nasal swabs. Methods: We defined as "nasal swab-related antibiotic protocol" the administration of a first-generation cephalosporin (cefazolin 2 g) in patients whose nasal swabs revealed the presence of normal nasal flora or methicillin-sensitive Staphylococcus aureus (MSSA), and the administration of vancomycin 1 g intravenously in patients whose nasal swabs revealed the presence of methicillin-resistant Staphylococcus aureus (MRSA) or with reported cephalosporin/penicillin allergy. This case-control study included 120 patients who underwent EESBS. The case group included 60 cases who received the "nasal swab-related antibiotic protocol," while the control group included 60 cases who received the "standard hospital antibiotic protocol" used in neurosurgery (cefazolin 2 g plus metronidazole 500 mg at induction, and 2 g of cefazolin repeated after 180 min). Results: The preoperative microbiological nasal swabs showed normal nasal flora in 42 patients (70%), MSSA in 17 patients (28.3%), and MRSA in 1 patient (1.6%). During the study period, no cases of meningitis or sinusitis occurred in the case group ("nasal swab-related antibiotic protocol"), while two infections (3.3%, 1 sinusitis and 1 meningitis) were reported in the control group ("standard hospital antibiotic protocol"). Mean length of hospitalization was 6.5 days for the case group and 8.5 days in the control group. "Standard hospital antibiotic protocol" is less expensive (range, 2.88–5.42 euros) compared with our new "nasal swab-related antibiotic protocol" (range, 10.02–32.56 euros), but in line with other antibiotic prophylaxis protocols reported in literature. Discussion: The low complication rates of our case series (0%) is comparable to complication rates reported in literature (1.6% for meningitis and 8% for sinusitis). Compared with other perioperative antibiotic regimens reported in literature, the "nasal swab-related antibiotic protocol" is cheap and at least equally effective. We discuss the rationale on which we based the choice of chemoprophylaxis, the timing, and the length of our regimen. Conclusions: Our study confirmed the safety and efficacy of our easily applicable and low-cost antibiotic prophylaxis protocol. [ABSTRACT FROM AUTHOR]

Equine adenovirus 1 (EAdV-1) can cause upper respiratory disease in horses and has been reported worldwide. In this study, and for the first time in Korea, the prevalence of EAdV-1 in equine nasal swabs was investigated using a PCR to identify potential risk factors and examine the genetic diversity of its DNA sequences by a comparison with foreign strains. Nasal swabs collected from 359 horses reared at Korea Racing Authority facilities were tested using an EAdV-1 hexon-specific PCR and the associations between EAdV-1 infection and sex, age, region, breed, and activity were analyzed. Five samples (1.4%, 5/359) tested positive for EAdV-1; however, no statistically significant differences were observed with respect to any variable. Among the five EAdV-1-positive horses, a co-infection with equine influenza, equine herpesvirus 1 and 4, or Streptococcus equi was not detected; however, clinical respiratory signs were observed in one. Phylogenetic analyses based on partial EAdV-1 hexon gene sequences revealed that the Korean EAdV-1 isolates shared approximately 98.8–100% similarity among each other and with foreign strains. Three Korean isolates shared high similarity with strains from Australia and India and the remaining two isolates were separate in phylogenetic analyses. These findings highlight the molecular prevalence and genetic diversity of EAdV-1 in horses in Korea.

Background and purpose: Methicillin resistant Staphylococcus aureus (MRSA) is a multidrug resistant organism emerging as a major cause of hospital acquired infection. In a healthcare setup a patient may acquire MRSA through the hands, clothes and equipments of health care workers. Screening of health care workers colonised with MRSA will be helpful in preventing the spread of this organism in a hospital. With this background the present study was undertaken to estimate the carriage rate of MRSA among healthcare workers in our hospital. Materials and Methods: Nasal swabs were collected from 430 health care workers working in SAIMS Medical College, Indore, during the study period of July-August 2019. The swabs were inoculated onto blood agar and mannitol salt agar plates for isolation of Staphylococcus aureus. MRSA strains were identified by cefoxitin disc method. Results: The prevalence of MRSA carriage among health care workers was 8.4% with the carrier rate being highest among nurses ,10%. 430 HCWs were screened for MRSA, among 430 HCWs, 37%were nurses, 56% were doctors and 7% were housekeeping staff. From the 430 nasal swab samples, 36% Staphylococcus aureus were isolated. Conclusions: Although the prevalence of MRSA among health care workers in our hospital is not alarming, it is important to emphasize the need for stringent hospital infection control policies to reduce the spread of MRSA to susceptible individuals. [ABSTRACT FROM AUTHOR]

Porcine respirovirus 1 (PRV1) is also known as porcine parainfluenza virus 1 (PPIV1). The prevalence and the role of PRV1 infections for pig health is largely unknown. In order to assess the PRV1 prevalence in Poland, nasal swabs and oral fluids collected from pigs from 30 farms were examined with RT real-time PCR. Additionally, IAV and PRRSV infection statuses of PRV1-positive samples were examined. The results showed that the virus is highly prevalent (76.7% farms positive) and different patterns of PRV1 circulation in herds with mild–moderate respiratory disease were observed. Co-infections with IAV and PRRSV were infrequent and detected in 8 (23.5%) and 4 (11.8%) out of 34 PRV1-positive nasal swab pools from diseased pens, respectively. In one pen PRV1, IAV, and PRRSV were detected at the same time. Interestingly, PRV1 mean Ct value in samples with co-infections was significantly lower (29.8 ± 3.1) than in samples with a single PRV1 infection (32.5 ± 3.6) (p < 0.05), which suggested higher virus replication in these populations. On the other hand, the virus detection in pig populations exhibiting respiratory clinical signs, negative for PRRSV and IAV, suggests that PRV1 should be involved in differential diagnosis of respiratory problems.

Madin–Darby canine kidney (MDCK) cells are commonly used for the isolation of mammalian influenza A viruses. The goal of this study was to compare the sensitivity and suitability of the original MDCK cell line in comparison with MDCK-derived cell lines, MDCK.2, MDCK SIAT-1 and MDCK-London for isolation of swine-origin influenza A viruses (IAV-S) from clinical specimens. One-hundred thirty clinical specimens collected from pigs in the form of nasal swabs, lung tissue and oral fluids that were positive by PCR for the presence of IAV-S RNA were inoculated in the cell cultures listed above. MDCK-SIAT1 cells yielded the highest proportion of positive IAV-S isolations from all specimen types. For nasal swabs, 58.62% of the specimens were IAV-S positive in MDCK-SIAT1 cells, followed by MDCK-London (36.21%), and conventional MDCK and MDCK.2 cells (27.5%). For lung specimens, 59.38% were IAV-S positive in MDCK-SIAT1 cells, followed by MDCK-London (40.63%), and conventional MDCK and MDCK.2 cells (18.75–31.25%). Oral fluids yielded the lowest number of positive virus isolation results, but MDCK-SIAT1 cells were still had the highest rate (35%) of IAV-S isolation, whereas the isolation rate in other cells ranged from 5–7.5%. Samples with lower IAV-S PCR cycle threshold (Ct) values were more suitable for culturing and isolation. The isolated IAV-S represented H1N1-β, H1N2-α, H1N1pdm and H3N2 cluster IV and cluster IVB viruses. The result of the current study demonstrated the importance of using the most appropriate MDCK cells when isolating IAV-S from clinical samples.