Influence of SARS-CoV-2 variants on COVID-19 epidemiological and clinical profiles: a comparative analysis of two waves of cases.

BACKGROUND: The COVID-19 pandemic has been the most significant health challenge of the last century. Multiple and successive waves of COVID-19 cases, driven particularly by the emergence of new SARS-CoV-2 variants, have kept the world in a constant state of alert. METHODS: We present an observational, descriptive, cross-sectional study aimed at identifying SARS-CoV-2 variants circulating during two local waves of COVID-19 cases in southern Bahia, Brazil (late 2021 and late 2022), and analyzing the association between the detected variants and the epidemiological and clinical characteristics of the disease. For this purpose, data and nasopharyngeal samples from individuals in southern Bahia, Brazil, with suspected COVID-19 were included. Viral detection was performed by RT-qPCR, and SARS-CoV-2 variants were identified by next-generation viral sequencing. RESULTS: A total of 368 nasopharyngeal samples were tested. Approximately 23% of the samples from late 2021 tested positive for SARS-CoV-2, while in 2022, the positivity rate was about 56%. All sequenced samples from 2021 were identified as the Delta variant, while in 2022, all samples were classified as the Omicron variant. Overall, individuals who tested positive for SARS-CoV-2 in 2022 were younger than those who tested positive in 2021. Moreover, we observed significant differences in the clinical spectrum of SARS-CoV-2 infection when comparing the two periods. Individuals who presented with anosmia/ageusia were more likely to test positive for SARS-CoV-2 infection in 2021 but not in 2022. Additionally, fever, dry cough, pharyngalgia, headache, and rhinorrhea were more frequent among individuals infected with the Omicron variant than among those infected with the Delta variant. CONCLUSIONS: The profile of COVID-19 in southern Bahia differed when analyzing two distinct waves of the pandemic in the region. These differences are likely related to the variants, which may differ in transmissibility and virulence, thereby altering the dynamics of the pandemic. This underscores the importance of genomic surveillance in better understanding the behavior of viral infections.

Single priming and a booster dose of 10-valent and 13-valent pneumococcal conjugate vaccine (PCV) maintains suppression of vaccine serotype colonization in South African children at 3, 4, and 5 years of age: a single-centre, open-labelled, randomized trial.

BACKGROUND: Surveillance on nasopharyngeal Streptococcus pneumoniae carriage in older children would be informative in determining whether a single priming and booster dose of pneumococcal conjugate vaccine (PCV) provides durable protection against pneumococcal disease compared with traditional dosing schedules. METHODS AND OBJECTIVES: We report on the secondary study objective to evaluate overall, vaccine-serotype (VT), and non-vaccine serotype (NVT) S. pneumoniae colonization at 3, 4, and 5 years of age in children who were randomized to receive 10-valent or 13-valent PCV formulations at 6 (6w + 1) or 14 (14w + 1) weeks compared with a two-dose primary series (2 + 1), with all children receiving a booster dose at 9 months of age, using a multiplex nanofluidic qPCR assay. RESULTS: The prevalence of overall, VT, or NVT at 5 years of age between the 2 + 1 compared with the 6w + 1 or 14w + 1 groups for both PCV10 and PCV13 did not differ. CONCLUSION: Although inconclusive, our findings suggest that a reduced 1 + 1 PCV dosing schedule is unlikely to increase breakthrough cases of VT pneumococcal disease in older children, which can inform decision-making on transitioning to a 1 + 1 schedule in South Africa.Clinical trial registration: The trial is registered at www.clinicaltrials.gov (identifier is NCT04275284).

Correlation of COVID-19 vaccination and RT-PCR ct value among cases in Addis Ababa, Ethiopia: implication for future preparedness.

BACKGROUND: The COVID-19 disease requires accurate diagnosis to effectively manage infection rates and disease progression. The study aims to assess the relationship between vaccination status and RT-PCR cycle threshold (Ct) values by comparing clinical, RDT and RT-PCR results. METHODS: A total of 453 suspected COVID-19 cases were included in this study. Nasopharyngeal swabs were collected for both RDT and RT-PCR testing, with RDTs conducted on-site and RT-PCR at the Ethiopian Public Health Institute (EPHI) genomics laboratory. Detailed clinical, RDT, and RT-PCR results were analyzed. Data analysis included descriptive statistics, cross-tabulation, and Chi-Square tests to investigate the connections between diagnostic outcomes and vaccination status, with a focusing on Ct values. RESULTS: RDT results showed 34.0% negative and 65.8% positive, while RT-PCR results indicated 35.8% negative and 64.2% positive cases. The discrepancies between RDT and RT-PCR results emphasize the importance of thorough testing. No significant association was found between vaccination status and viral load, as indicated by Ct values. Among RT-PCR positive cases, 49.8% had been vaccinated, suggesting challenges in interpreting results among vaccinated individuals. Further analysis revealed that vaccination (first or second dose) had minimal impact on Ct values, indicating limited influence of vaccination status on viral load dynamics in infected individuals. CONCLUSIONS: The study highlights the significant differences between RDT and RT-PCR outcomes, underscoring the need for a comprehensive testing approach. Additionally, the findings suggest that vaccination status does not significantly impact RT-PCR Ct values, complicating the interpretation of diagnostic results in vaccinated individuals, especially in breakthrough infections and potential false positives.

Point-of-care testing for COVID-19: a simple two-step molecular diagnostic development and validation during the SARS-CoV-2 pandemic.

BACKGROUND: During the coronavirus disease 19 (COVID-19) pandemic, diagnostic testing of the general population proved challenging due to limitations of the gold-standard diagnostic procedure using reverse transcription real-time polymerase chain reaction (RT-qPCR) for large-scale testing on the centralised model, especially in low-resource areas. OBJECTIVES: To address this, a point-of-care (PoC) diagnostic protocol for COVID-19 was developed, providing fast, reliable, and affordable testing, particularly for low-mid develop areas. METHODS: The PoC diagnostic process combines a simple paper-based RNA extraction method housed within a 3D-printed plastic device with a colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay. Nasopharyngeal/oropharyngeal swabs (NOS) and saliva samples were tested between 2020 and 2021, with the assistance of Santa Catarina's State Health Secretary, Brazil. FINDINGS: The developed diagnostic protocol showed a limit of detection of 9,900 copies and an overall diagnostic specificity of 98% for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from 1,348 clinical analysed samples. The diagnostic sensitivity was 95% for NOS samples, 85% for early morning saliva, and 69% for indiscriminate saliva. MAIN CONCLUSIONS: In conclusion, the developed device successfully extracted SARS-CoV-2 viral RNA from swabs and saliva clinical samples. When combined with colorimetric RT-LAMP, it provides results within 45 min using minimal resources, thus delivering a diagnostic kit protocol that is applicable in large-scale sampling.

Design and implementation of a metagenomic analytical pipeline for respiratory pathogen detection.

OBJECTIVE: We developed an in-house bioinformatics pipeline to improve the detection of respiratory pathogens in metagenomic sequencing data. This pipeline addresses the need for short-time analysis, high accuracy, scalability, and reproducibility in a high-performance computing environment. RESULTS: We evaluated our pipeline using ninety synthetic metagenomes designed to simulate nasopharyngeal swab samples. The pipeline successfully identified 177 out of 204 respiratory pathogens present in the compositions, with an average processing time of approximately 4 min per sample (processing 1 million paired-end reads of 150 base pairs). For the estimation of all the 470 taxa included in the compositions, the pipeline demonstrated high accuracy, identifying 420 and achieving a correlation of 0.9 between their actual and predicted relative abundances. Among the identified taxa, 27 were significantly underestimated or overestimated, including only three clinically relevant pathogens. We also validated the pipeline by applying it to a clinical dataset from a study on metagenomic pathogen characterization in patients with acute respiratory infections and successfully identified all pathogens responsible for the diagnosed infections. These findings underscore the pipeline's effectiveness in pathogen detection and highlight its potential utility in respiratory pathogen surveillance.

[The Molecular and Biological Patterns Underlying Sustained SARS-CoV-2 Circulation in the Human Population].

INTRODUCTION: For four years, SARS-CoV-2, the etiological agent of COVID-19, has been circulating among humans. By the end of the second year, an absence of immunologically naive individuals was observed, attributable to extensive immunization efforts and natural viral exposure. This study focuses on delineating the molecular and biological patterns that facilitate the persistence of SARS-CoV-2, thereby informing predictions on the epidemiological trajectory of COVID-19 toward refining pandemic countermeasures. The aim of this study was to describe the molecular biological patterns identified that contribute to the persistence of the virus in the human population. MATERIALS AND METHODS: For over three years since the beginning of the COVID-19 pandemic, molecular genetic monitoring of SARS-CoV-2 has been conducted, which included the collection of nasopharyngeal swabs from infected individuals, assessment of viral load, and subsequent whole-genome sequencing. RESULTS: We discerned dominant genetic lineages correlated with rising disease incidence. We scrutinized amino acid substitutions across SARS-CoV-2 proteins and quantified viral loads in swab samples from patients with emerging COVID-19 variants. Our findings suggest a model of viral persistence characterized by 1) periodic serotype shifts causing substantial diminutions in serum virus-neutralizing activity (> 10-fold), 2) serotype-specific accrual of point mutations in the receptor-binding domain (RBD) to modestly circumvent neutralizing antibodies and enhance receptor affinity, and 3) a gradually increasing amount of virus being shed in mucosal surfaces within a single serotype. CONCLUSION: This model aptly accounts for the dynamics of COVID-19 incidence in Moscow. For a comprehensive understanding of these dynamics, acquiring population-level data on immune tension and antibody neutralization relative to genetic lineage compositions is essential.

Palatal relaxing incisions versus nasopharyngeal relaxing incisions in Palatoplasty.

BACKGROUND: Bone denudation after conventional relaxing incisions could be a critical factor in inhibiting maxillofacial growth. To address this, alternative relaxing incisions were designed. Thus, this study aimed to compare the effectiveness of palatal relaxing incisions versus nasopharyngeal relaxing incisions in enhancing postoperative outcomes. MATERIALS AND METHODS: A retrospective cohort study was conducted, involving a total of 120 patients divided into three groups: 40 patients have received modified Furlow palatoplasty with nasopharyngeal relaxing incisions (M.F + N.P.I palatoplasty), and 40 patients who received modified Furlow palatoplasty with palatal relaxing incisions (M.F + P.R.I palatoplasty). The other 40 patients received original Furlow palatoplasty without relaxing incisions (F palatoplasty). Data collected included gender, cleft type, cleft width, age at repair, velopharyngeal function, presence of palatal fistula, and follow-up. The chi-square test compared frequencies of sex, cleft type, postoperative fistula, and velopharyngeal outcomes across groups. The Mann-Whitney and independent t-tests compared mean values, with statistical significance set at p < 0.05. RESULTS: The mean age at repair was similar across groups, with follow-up periods ranging from 5 to 11 years. No significant differences were found among the M.F + N.P.I and M.F + P.L.I groups regarding gender, cleft type, cleft width, and age at repair. However, the F group had a significantly narrowest cleft width compared to the other groups. Postoperative outcomes showed no significant differences in velopharyngeal function among the three groups, but the F group had a significantly higher rate of palatal fistula (32.5%) compared to the M.F + P.L.I (10%) and M.F + N.P.I (7.5%) groups. A comparison of the two modified Furlow techniques revealed no significant differences in velopharyngeal closure rates or the incidence of velopharyngeal insufficiency and persistent palatal fistula across different Veau classifications. CONCLUSIONS: While both incisions showed similar impacts on palatoplasty outcomes, palatal relaxing incisions may expose more bone and pose a higher risk of secondary healing issues. Therefore, nasopharyngeal relaxing incisions are recommended as an effective and potentially preferable technique in palatoplasty whenever feasible. CLINICAL RELEVANCE: The current study suggests that, whenever feasible, nasopharyngeal relaxing incisions are advised as an effective and potentially superior technique in palatoplasty.

Limited Short-Term Evolution of SARS-CoV-2 RNA-Dependent RNA Polymerase under Remdesivir Exposure in Upper Respiratory Compartments.

BACKGROUND: The extent of the SARS-CoV-2 short-term evolution under Remdesivir (RDV) exposure and whether it varies across different upper respiratory compartments are not fully understood. METHODS: Patients hospitalized for COVID-19, with or without RDV therapy, were enrolled and completed up to three visits, in which they provided specimens from four respiratory compartments. Near full-length genome SARS-CoV-2 sequences were obtained from viral RNA, standard lineage and variant assignments were performed, and viral mutations in the RNA-dependent RNA polymerase (RdRp) region-the RDV target gene-were detected and compared between participants with and without RDV, across the four compartments, within participants across visits, and versus a larger sequence dataset. The statistical analysis used a generalized linear mixed-effects model. RESULTS: A total of 139 sequences were obtained from 37 out of the 44 (84%) enrolled participants. The genotyping success varied across respiratory compartments, which ranged from 42% with oropharyngeal specimens to 67% with nasopharyngeal specimens and showed improvement with higher viral loads. No RdRp mutations known to be associated with RDV resistance were identified, and for 34 detected mutations at 32 amino acid positions that are not known as RDV-associated, there was no evidence of any associations with the RDV exposure, respiratory compartment, or time. At least 1 of these 34 mutations were detected in all participants, and some differed from the larger sequence dataset. CONCLUSIONS: This study highlighted the SARS-CoV-2 short-term genomic stability within hosts and across upper respiratory compartments, which suggests a lack of evolution of RDV resistance over time. This contributes to our understanding of SARS-CoV-2 genomic dynamics.

The Role of Quantitative PCR in Evaluating the Clinical Significance of Human Bocavirus Detection in Children.

Human bocavirus (HBoV) has emerged as a significant pathogen primarily associated with respiratory infections in children. This study aimed to evaluate the clinical relevance of HBoV infection by quantifying viral loads in nasopharyngeal swabs from hospitalized children with acute respiratory infections (ARIs) and investigating correlations with clinical outcomes. A total of 957 children were tested, with HBoV detected in 73 cases (7.6%), either as a sole infection or co-infection with other respiratory viruses. Quantitative polymerase chain reaction (qPCR) was employed to measure viral load, and a threshold of 104 copies/mL was used to differentiate high and low viral concentrations. Results have shown that children with lower respiratory tract infections (LRTIs) had significantly higher viral loads, most notably in cases where HBoV was the sole pathogen. Additionally, children with pre-existing health conditions were more likely to have elevated HBoV concentrations compared to those who were previously healthy. Children with higher viral loads were more likely to require oxygen supplementation and receive empirical antibiotic therapy, indicating a more severe clinical course. This study underscores the importance of considering HBoV viral load in clinical diagnostics, as higher concentrations were associated with more severe presentations, including the need for oxygen support. Future research should focus on refining diagnostic thresholds and exploring HBoV's role in co-infections to enhance patient care strategies.

Atorvastatin and telmisartan do not reduce nasopharyngeal carriage of SARS-CoV-2 in mild or moderate COVID-19 in a phase IIb randomized controlled trial.

Observational studies suggest a reduction in fatal or severe COVID-19 disease with the use of ACE2 inhibitors and statins. We implemented a randomized controlled tree-arm open label trial evaluating the benefits of adding telmisartan (TLM) or atorvastatin (ATV) to lopinavir boosted ritonavir (LPVr) on the SARS-CoV-2 nasopharyngeal viral load in patients with mild / moderate COVID-19 infection in Côte d'Ivoire. RT-PCR positive COVID-19 patients ≥ 18 years, with general or respiratory symptoms for less than 7 days were randomized (1:1:1) to receive LPVr (400 mg/100 mg twice daily), LPVr + TLM (10 mg once daily) or LPVr + ATV (20 mg once daily) for 10 days. The primary endpoint was viro-inflammatory success defined as a composite variable at day 11: Ct ≥ 40 and C-reactive protein < 27 mg/L. We randomized 294 patients: 96 to LPVr, 100 to LPVr + TLM, 98 to LPVr + ATV arms. Baseline characteristics were well balanced between arms. In the primary analysis (missing = failure), 46% patients in the LPVr arm reached viro-inflammatory success at day 11 vs 43% in the LPVr + TLM arm (p = 0.69) and 43% in the LPVr + ATV arm (p = 0.68). The median time from baseline to resolution of COVID-19 related symptoms was not different between arms. Nine patients were hospitalized: 2 in the LPVr arm, 5 in the LPVr + TLM arm and 2 in the LPVr + ATV arm and 4 patients died. Among adults with mild to moderate COVID-19 infection, the addition of telmisartan or atorvastatin, to the standard LPVr treatment is not associated with a better virological or clinical outcome.Trial registration: NCT04466241, registered on 10/07/2020.

Nasopharyngeal carriage rate, antimicrobial susceptibility pattern, and associated risk factors of Streptococcus pneumoniae among children in Ethiopia: a systematic review and meta-analysis.

BACKGROUND: Nasopharyngeal carriage of S. pneumoniae is a global health problem that has been associated with the emergence of severe disease and pathogen dissemination in the community. However, summary data on the carriage rate, antimicrobial susceptibility profile, and determinant factors is lacking. METHOD: Articles were extensively searched in bibliographic databases and gray literature using entry terms or phrases. Studies meeting eligibility criteria were extracted in MS Excel and exported to STATA version 17 software for statistical analysis. A random-effects model was used to compute the pooled magnitude of the nasal carriage of S. pneumoniae and its multidrug resistance. The heterogeneity was quantified by using the I2 value. Publication bias was assessed using a funnel plot and Egger's test. Sensitivity analysis was done to assess the impact of a single study on the pooled effect size. RESULT: Of the 146 studies identified, 8 studies containing a total of 3223 children were selected for meta-analysis of the magnitude of the nasal carriage of S. pneumoniae and its multidrug resistance. The overall pooled prevalence of nasal carriage of S. pneumoniae and its MDR status in Ethiopian children was 32.77% (95%CI: 25.1, 40.44). and 31.22% (95%CI: 15.06, 46.84), respectively. The highest resistant pattern of S. pneumoniae was against tetracycline, which was 46.27% (95%CI: 37.75, 54.79), followed by 45.68% (95%CI: 34.43, 57.28) trimethoprim-sulfamethoxazole, while the least pooled prevalence was against chloramphenicol, which was 16.2% (95%CI: 9.44, 22.95). The pooled effect of age less than 5 years old (pooled OR = 1.97; 95% CI: 1.35, 2.88, P < 0.001), co-sleeping habit with others (pooled OR = 2.36; 95% CI: 1.77, 3.66; P < 0.001), sibling (pooled OR = 1.82; 95% CI: 1.14, 2.91, P = 0.01), history of hospitalization (pooled OR = 4.39; 95% CI: 1.86, 10.34, P = 0.001), and malnutrition (pooled OR = 2.18; 95% CI: 1.49, 3.19; P < 0.001) showed a statistical association with S. pneumoniae nasal carriage rate by using the random effect Sidik-Jonkman model. CONCLUSION: The magnitude of the nasopharyngeal carriage rate and multi-drug resistance status of S. pneumoniae alarms the need for immediate interventions such as strengthening antimicrobial stewardship programs, undertaking national antimicrobial surveillance, one-health initiatives, and national immunization programs.

Emergence of the B.1.214.2 SARS-CoV-2 lineage with an Omicron-like spike insertion and a unique upper airway immune signature.

We investigate the emergence, mutation profile, and dissemination of SARS-CoV-2 lineage B.1.214.2, first identified in Belgium in January 2021. This variant, featuring a 3-amino acid insertion in the spike protein similar to the Omicron variant, was speculated to enhance transmissibility or immune evasion. Initially detected in international travelers, it substantially transmitted in Central Africa, Belgium, Switzerland, and France, peaking in April 2021. Our travel-aware phylogeographic analysis, incorporating travel history, estimated the origin to the Republic of the Congo, with primary European entry through France and Belgium, and multiple smaller introductions during the epidemic. We correlate its spread with human travel patterns and air passenger data. Further, upon reviewing national reports of SARS-CoV-2 outbreaks in Belgian nursing homes, we found this strain caused moderately severe outcomes (8.7% case fatality ratio). A distinct nasopharyngeal immune response was observed in elderly patients, characterized by 80% unique signatures, higher B- and T-cell activation, increased type I IFN signaling, and reduced NK, Th17, and complement system activation, compared to similar outbreaks. This unique immune response may explain the variant's epidemiological behavior and underscores the need for nasal vaccine strategies against emerging variants.

Unveiling viral pathogens in acute respiratory disease: Insights from viral metagenomics in patients from the State of Alagoas, Brazil.

BACKGROUND: Respiratory illness affects individuals across all age demographics on a global scale, often precipitated by viral infections. The symptomatic manifestations of these diseases bear clinical resemblance, complicating the accurate determination of their etiological origins. Furthermore, the diagnostic panels for respiratory pathogens used within local medical practices, may not encompass the full spectrum of viral agents responsible for such ailments. Consequently, a significant number of clinically important viral pathogens may remain undetected. METHODS AND FINDINGS: In the light of this, we conducted a metagenomic examination of 66 nasopharyngeal swab specimens, obtained from patients presenting with acute respiratory conditions yet tested negative by the standard diagnostic panels available locally. These specimens were obtained from the Public Health Laboratory, Maceio, State of Alagoas. Our findings indicate a predominant diagnostic escape of rhinoviruses and notably enterovirus D68. Moreover, our study identified a substantial quantity of sequence reads attributed to human respirovirus 3 (human parainfluenza 3) along with various herpresviruses including human herpesvirus-1, Epstein-Barr virus (Human herpesvirus-4), Human herpesviruses 6 and 7 and human parvovirus B19 (B19V). Notably, the metagenomic analysis uncovered a widespread presence of the emerging human vientovirus FB in most of sample pools, though its clinical importance remains to be elucidated. CONCLUSIONS: The obtained results in this study underscore the invaluable role of viral metagenomics in the identification of underrecognized viruses bearing clinical relevance. Furthermore, it offers insights into the dissemination of these pathogens within the studied area, thereby informing public health strategies aimed at enhancing diagnostic accuracy and improving patient care.

Estimating pneumococcal carriage dynamics in adults living with HIV in a mature infant pneumococcal conjugate vaccine programme in Malawi, a modelling study.

BACKGROUND: Adults living with human immunodeficiency virus (ALWHIV) receiving antiretroviral therapy (ART) exhibit higher pneumococcal carriage prevalence than adults without HIV (HIV-). To assess factors influencing high pneumococcal carriage in ALWHIV, we estimated pneumococcal carriage acquisition and clearance rates in a high transmission and disease-burdened setting at least 10 years after introducing infant PCV13 in routine immunisation. METHODS: We collected longitudinal nasopharyngeal swabs from individuals aged 18-45 in Blantyre, Malawi. The study group included both HIV- individuals and those living with HIV, categorised based on ART duration as either exceeding 1 year (ART > 1y) or less than 3 months (ART < 3 m). Samples were collected at baseline and then weekly for 16 visits. To detect pneumococcal carriage, we used classical culture microbiology, and to determine pneumococcal serotypes, we used latex agglutination. We modelled trajectories of serotype colonisation using multi-state Markov models to capture pneumococcal carriage dynamics, adjusting for age, sex, number of under 5 year old (< 5y) children, social economic status (SES), and seasonality. RESULTS: We enrolled 195 adults, 65 adults in each of the study groups. 51.8% were females, 25.6% lived with more than one child under 5 years old, and 41.6% lived in low socioeconomic areas. The median age was 33 years (IQR 25-37 years). The baseline pneumococcal carriage prevalence of all serotypes was 31.3%, with non-PCV13 serotypes (NVT) at 26.2% and PCV13 serotypes (VT) at 5.1%. In a multivariate longitudinal analysis, pneumococcal carriage acquisition was higher in females than males (hazard ratio [HR], NVT [1.53]; VT [1.96]). It was also higher in low than high SES (NVT [1.38]; VT [2.06]), in adults living with 2 + than 1 child < 5y (VT [1.78]), and in ALWHIV on ART > 1y than HIV- adults (NVT [1.43]). Moreover, ALWHIV on ART > 1y cleared pneumococci slower than HIV- adults ([0.65]). Residual VT 19F and 3 were highly acquired, although NVT remained dominant. CONCLUSIONS: The disproportionately high point prevalence of pneumococcal carriage in ALWHIV on ART > 1y is likely due to impaired nasopharyngeal clearance, which results in prolonged carriage. Our findings provide baseline estimates for comparing pneumococcal carriage dynamics after implementing new PCV strategies in ALWHIV.

Validation of Saliva as the Clinical Specimen Type for a University-Wide COVID-19 Surveillance Program.

At the beginning of the COVID-19 pandemic, the Georgia Institute of Technology made the decision to keep the university doors open for on-campus attendance. To manage COVID-19 infection rates, internal resources were applied to develop and implement a mass asymptomatic surveillance program. The objective was to identify infections early for proper follow-on verification testing, contact tracing, and quarantine/isolation as needed. Program success depended on frequent and voluntary sample collection from over 40,000 students, faculty, and staff personnel. At that time, the nasopharyngeal (NP) swab, not saliva, was the main accepted sample type for COVID-19 testing. However, due to collection discomfort and the inability to be self-collected, the NP swab was not feasible for voluntary and frequent self-collection. Therefore, saliva was selected as the clinical sample type and validated. A saliva collection kit and a sample processing and analysis workflow were developed. The results of a clinical sample-type comparison study between co-collected and matched NP swabs and saliva samples showed 96.7% positive agreement and 100% negative agreement. During the Fall 2020 and Spring 2021 semesters, 319,988 samples were collected and tested. The program resulted in maintaining a low overall mean positivity rate of 0.78% and 0.54% for the Fall 2020 and Spring 2021 semesters, respectively. For this high-throughput asymptomatic COVID-19 screening application, saliva was an exceptionally good sample type.

Epithelial Antimicrobial Peptide/Protein and Cytokine Expression Profiles Obtained from Nasopharyngeal Swabs of SARS-CoV-2-Infected and Non-Infected Subjects.

Immune responses of the epithelia of the upper respiratory tract are likely crucial in early inhibition of the viral replication and finally clearance of SARS-CoV-2. We aimed to compare the expression profiles of antimicrobial peptides/proteins (AMPs) and related cytokines observed in the nasopharynx of SARS-CoV-2-infected patients and non-infected controls and to assess the associations between these parameters and COVID-19 patients' outcomes. We included 45 subjects who had tested positive for SARS-CoV-2 and 22 control subjects who had tested negative for SARS-CoV-2. Biomaterial for SARS-CoV-2 detection, as well as gene and protein expression studies, was obtained from all subjects using nasopharyngeal swabs which were performed a maximum of 7 days before inclusion in the study. Univariable and multivariable statistics were performed. When compared to the controls, the mRNA expression levels of human ß-defensin 1 (hBD-1), LL-37, and trappin-2 were significantly higher in specimens of nasopharyngeal swabs from COVID-19 patients. Protein expression of hBD-1 was also increased in the COVID-19 group. mRNA expression levels of interferon-É£ (IFN-É£), tumor necrosis factor- ɑ (TNF-ɑ), and interleukin-6 (IL-6) measured in SARS-CoV-2-infected patients were significantly higher than those observed in the controls, which could also be confirmed in the protein levels of IFN-É£ and IL-6. A significant correlation between mRNA and protein levels could be observed only for IL-6. Univariable analysis revealed that low IFN-É£ mRNA levels were associated with severe/fatal outcomes. The occurrence of COVID-19 pneumonia was significantly associated with lower expression levels of IL-6 mRNA, IFN-É£ mRNA, and TNF-ɑ mRNA. Concerning the severe/fatal outcomes, the multivariable logistic regression model revealed that none of the aforementioned parameters remained significant in the model. However, the logistic regression model revealed that higher TNF-ɑ mRNA expression was a significant independent predictor of absence of pneumonia [odds ratio: 0.35 (95% CI 0.14 to 0.88, p = 0.024)]. In conclusion, nasopharyngeal expression of AMPs (hBD-1, LL-37, and trappin-2) and cytokines (IL-6, IFN-É£, and TNF-ɑ) is upregulated in response to early SARS-CoV-2 infection, indicating that these AMPs and cytokines play a role in the local host defense against the virus. Upregulated nasopharyngeal TNF-ɑ mRNA expression during the early phase of SARS-CoV-2 infection was a significant independent predictor of the absence of COVID-19 pneumonia. Hence, high TNF-ɑ mRNA expression in the nasopharynx appears to be a protective factor for lung complications in COVID-19 patients.

[Antimicrobial in vitro effects of eight essential oils on Pasteurella multocida and Mannheimia haemolytica from nasopharyngeal swab samples of fattening calves]. / Antimikrobielle in-vitro-Wirkung acht ätherischer Öle auf Pasteurella multocida und Mannheimia haemolytica aus Nasenrachentupferproben von Mastkälbern.

INTRODUCTION: Essential oils are secondary metabolites of aromatic plants and are used in phytotherapy to treat various diseases. In the present study, eight selected essential oils - ajwain oil (Trachyspermum ammi L.), fennel oil (Foeniculum vulgare Mill. subsp. vulgare var. vulgare), thyme oil chemotype (ct.) thymol (Thymus vulgaris L.), tea tree oil (Melaleuca alternifolia Cheel.), oregano oil (Origanum vulgare L.), mountain savory oil (Satureja montana L.), lemongrass oil (Cymbopogon citratus (DC.) Stapf.) and eucalyptus oil (Eucalyptus globulus Labill.) -were examined for their antibacterial effect against Pasteurella (P.) multocida and Mannheimia (M.) haemolytica isolates from deep nasopharyngeal swab samples of fattening calves using agar diffusion and microdilution. All eight essential oils were effective against the tested isolates. Lemongrass oil proved to be the most potent of all eight essential oils, while fennel oil was only weakly effective. Different antimicrobial effects were observed between the two research methods. The effectiveness of ajwain, thyme, oregano and mountain savory oils was comparable in agar diffusion. However, this could not be reproduced using the microdilution method. P. multocida was found to be more sensitive to all essential oils tested than M. haemolytica. This study shows that the tested essential oils have antimicrobial in-vitro effects on P. multocida and M. haemolytica isolates and that the examination method is associated with the test result.

INTRODUCTION: Les huiles essentielles sont des métabolites secondaires de plantes aromatiques et sont utilisées en phytothérapie pour le traitement de différentes maladies. Dans la présente étude, huit huiles essentielles sélectionnées ­ huile d'ajowan (Trachyspermum ammi L.), huile de fenouil (Foeniculum vulgare Mill. subsp. vulgare var. vulgare), huile de thym chémotype (ct.) thymol (Thymus vulgaris L.), huile d'arbre à thé (Melaleuca alternifolia Cheel.), huile d'origan (Origanum vulgare L.), huile de sarriette de montagne (Satureja montana L. ), huile de citronnelle (Cymbopogon citratus (DC.) Stapf.) et huile d'eucalyptus (Eucalyptus globulus Labill.) ­ ont été étudiées par diffusion sur gélose et microdilution pour leur effet antibactérien sur des isolats de Pasteurella (P.) multocida et de Mannheimia (M.) haemolytica provenant d'échantillons d'écouvillons nasaux profonds de veaux d'engraissement. Les huit huiles essentielles se sont révélées efficaces sur les isolats testés. L'huile de citronnelle s'est avérée être la plus puissante des huit huiles essentielles, tandis que l'huile de fenouil n'était que faiblement efficace. Des effets différents ont été observés entre les deux méthodes de recherche utilisées. Par exemple, l'efficacité des huiles d'ajowan, de thym, d'origan et de sarriette de montagne était comparable dans la diffusion sur gélose. Cependant, cela n>a pas pu être reproduit avec la méthode de microdilution. P. multocida s'est révélée plus sensible que M. haemolytica à toutes les huiles essentielles testées. Cette étude montre premièrement que les huiles essentielles testées ont une efficacité antimicrobienne in vitro sur des isolats cliniques de P. multocida et de M. haemolytica. Deuxièmement, elle montre que la méthode d'examen est associée au résultat du test.

Changes in the upper airway and its surrounding structures after bimaxillary surgery in patients with cleft-related Class III deformity.

OBJECTIVES: To compare upper airway changes following bimaxillary surgery for correction of Class III deformity between patients with unilateral cleft lip and palate (UCLP) and bilateral cleft lip and palate (BCLP) and to compare the preoperative and postoperative upper airway among patients with UCLP and BCLP to healthy controls. MATERIALS AND METHODS: Sixty adults with CLP-related skeletal Class III deformity (30 UCLP and 30 BCLP) who consecutively underwent bimaxillary surgery were studied retrospectively. Cone-beam computed tomography (CBCT) was performed before and after surgery to measure upper airway and movements of facial skeletal and surrounding structures. CBCT images from 30 noncleft skeletal Class I adults, matched by age, gender, and body mass index and without surgical intervention, served as controls. RESULTS: After surgery, the volume of the nasopharynx increased in patients with CLP (both P < .001). Patients with CLP did not differ from controls in postoperative volume of the nasopharynx or oropharynx. However, the nasal cavity differed significantly between patients with CLP and controls (P < .001). CONCLUSIONS: After bimaxillary surgery, the nasal cavity of patients with CLP differed significantly compared with the controls. Volumes of the nasopharynx and oropharynx did not differ between patients with CLP after surgery and controls.

Æ©S COVID-19 is a rapid high throughput and sensitive one-step quadruplex real-time RT-PCR assay.

Real-time reverse transcription polymerase chain reaction (RT-PCR), a standard method recommended for the diagnosis of coronavirus disease 2019 (COVID-19) requires 2-4 h to get the result. Although antigen test kit (ATK) is used for COVID-19 screening within 15-30 min, the drawback is its limited sensitivity. Hence, a rapid one-step quadruplex real-time RT-PCR assay: termed Æ©S COVID-19 targeting ORF1ab, ORF3a, and N genes of SARS-CoV-2; and Avocado sunblotch viroid (ASBVd) as an internal control was developed. Based on strategies including designing high melting temperature primers with short amplicons, applying a fast ramp rate, minimizing hold time, and reducing the range between denaturation and annealing/extension temperatures; the assay could be accomplished within 25 min. The limit of detection of ORF1ab, ORF3a, and N genes were 1.835, 1.310, and 1 copy/reaction, respectively. Validation was performed in 205 combined nasopharyngeal and oropharyngeal swabs. The sensitivity, specificity, positive predictive value, and negative predictive value were 92.8%, 100%, 100%, and 97.1%, respectively with 96.7% accuracy. Cohen's Kappa was 0.93. The newly developed rapid real-time RT-PCR assay was highly sensitive, specific, and fast, making it suitable for use as an alternative method to support laboratory diagnosis of COVID-19 in outpatient and emergency departments.

Epidemiology and genetic characterization of human parainfluenza virus-1 infection in pediatric patients from Hangzhou China, 2021-2022.

BACKGROUND: Human parainfluenza virus-1 (HPIV-1) is a notable pathogen instigating acute respiratory tract infections in children. The article is to elucidate the epidemiological and genetic characteristics of HPIV-1 circulating in Hangzhou during the period of 2021-2022. METHODS: A cohort of 2360 nasopharyngeal swabs were amassed and subsequently examined via RT-PCR, with HPIV-1 positive samples undergoing P gene sequencing. RESULTS: The highest HPIV-1 infection rates were found in children aged between 3 and 6 years. A pronounced positive rate persisted through the latter half of 2021, with a notable decline observed in the initial half of 2022. All HPIV-1 strains could be clustered into 2 groups: Cluster 1, with strains similar to those found in Japan (LC764865, LC764864), and Cluster 2, with strains similar to the Beijing strain (MW575643). CONCLUSION: In conclusion, our study contributes to the comprehensive data on the epidemiological and genetic characteristics of HPIV-1 in pediatric patients from Hangzhou, post the COVID-19 peak.