A novel metric-based approach of scoring early host immune response from oro-nasopharyngeal swabs predicts COVID-19 outcome.

Unpredictable fatal outcome of COVID-19 is attributed to dysregulated inflammation. Impaired early adaptive immune response leads to late-stage inflammatory outcome. The purpose of this study was to develop biomarkers for early detection of host immune impairment at first diagnosis from leftover RNA samples, which may in turn identify high risk patients. Leftover RNA samples of COVID-19 patients at first diagnosis were stored. Following prospective follow-up, the samples were shorted and categorized into outcome groups. Impaired adaptive T cell response (severity score) and Impaired IL-10 response (undetectable IL-10 in the presence of high expression of a representative interferon response gene) were determined by RT-PCR based assay. We demonstrate that a T cell response based 'severity score' comprising rational combination of Ct values of a target genes' signature can predict high risk noncomorbid potentially critical COVID-19 patients with a sensitivity of 91% (95% CI 58.7-99.8) and specificity of 92.6% (95% CI 75.7-99) (AUC:0.88). Although inclusion of comorbid patients reduced sensitivity to 77% (95% CI 54.6-92.2), the specificity was still 94% (95% CI 79.8-99.3) (AUC:0.82). The same for 'impaired IL-10 response' were little lower to predict high risk noncomorbid patients 64.2% (95% CI 35.1-87.2) and 82% (95% CI 65.5-93.2) respectively. Inclusion of comorbid patients drastically reduce sensitivity and specificity51.6% (95% CI 33.1-69.8) and 80.5% (95% CI 64.0-91.8) respectively. As best of our knowledge this is the first demonstration of a metric-based approach showing the 'severity score' as an indicator of early adoptive immune response, could be used as predictor of severe COVID-19 outcome at the time of first diagnosis using the same leftover swab RNA. The work flow could reduce expenditure and reporting time of the prognostic test for an earliest clinical decision ensuring possibility of early rational management.

Detection of lumpy skin disease virus reads in the human upper respiratory tract microbiome requires further investigation.

Lumpy skin disease virus (LSDV), a double-stranded DNA virus from the Capripoxvirus genus, primarily affects Bos indicus, Bos taurus breeds, and water buffalo. Arthropod vectors, including mosquitoes and biting flies, are the main LSDV transmitters. Although LSDV is not zoonotic, this study unexpectedly detected LSDV reads in the upper respiratory tract microbiome of humans from rural and urban areas in Maharashtra, India. Nasopharyngeal and oropharyngeal swab samples collected for SARS-CoV-2 surveillance underwent whole-genome metagenomics sequencing, revealing LSDV reads in 25% of samples. Split kmer analysis provided insights into sample relatedness despite the low coverage of LSDV reads with the reference genome. Our findings, which include the detection of LSDV contigs aligning to specific locations on the reference genome, suggest a common source for LSDV reads, potentially shared water sources, or milk/milk products. Further investigation is needed to ascertain the mode of transmission and reason for the detection of LSDV reads in human upper respiratory tract.

Next-Generation Sequencing for Characterizing Respiratory Tract Virome and Improving Detection of Viral Pathogens in Children With Pneumonia.

BACKGROUND: Pneumonia is typically caused by a variety of pathogenic microorganisms. Traditional research often focuses on the infection of a few microorganisms, whereas metagenomic studies focus on the impact of the bacteriome and mycobiome on respiratory diseases. Reports on the virome characteristics of pediatric pneumonia remain relatively scarce. METHODS: We employed de novo assembly and combined homology- and feature-based methods to characterize the respiratory virome in whole-genome DNA sequencing samples from oropharynx (OP) swabs, nasopharynx (NP) swabs, and bronchoalveolar lavage fluids (BALF) of children with pneumonia. RESULTS: Significant differences were observed in the alpha and beta diversity indexes, as well as in the composition of the oropharyngeal virome, between pneumonia cases and controls. We identified 1137 viral operational taxonomic units (vOTUs) with significant differences, indicating a preference of pneumonia-reduced vOTUs for infecting Prevotella, Neisseria, and Veillonella, whereas pneumonia-enriched vOTUs included polyomavirus, human adenovirus, and phages targeting Staphylococcus, Streptococcus, Granulicatella, and Actinomyces. Comparative analysis revealed higher relative abundances and prevalence rates of pneumonia-enriched OP vOTUs in NP and BALF samples compared to pneumonia-reduced vOTUs. Additionally, virome analysis identified six pediatric patients with severe human adenovirus or polyomavirus infections, five of whom might have been undetected by targeted polymerase chain reaction (PCR)-based testing. CONCLUSIONS: This study offers insights into pediatric pneumonia respiratory viromes, highlighting frequent transmission of potentially pathogenic viruses and demonstrating virome analysis as a valuable adjunct for pathogen detection.

Comparative analysis of oropharyngeal microbiota in healthcare workers post-COVID-19.

Background: To date, more than 770 million individuals have become coronavirus disease 2019 (COVID-19) convalescents worldwide. Emerging evidence highlights the influence of COVID-19 on the oral microbiome during both acute and convalescent disease phases. Front-line healthcare workers are at an elevated risk of exposure to viral infections, and the effects of COVID-19 on their oral microbiome remain relatively unexplored. Methods: Oropharyngeal swab specimens, collected one month after a negative COVID-19 test from a cohort comprising 55 healthcare workers, underwent 16S rRNA sequencing. We conducted a comparative analysis between this post-COVID-19 cohort and the pre-infection dataset from the same participants. Community composition analysis, indicator species analysis, alpha diversity assessment, beta diversity exploration, and functional prediction were evaluated. Results: The Shannon and Simpson indexes of the oral microbial community declined significantly in the post-COVID-19 group when compared with the pre-infection cohort. Moreover, there was clear intergroup clustering between the two groups. In the post-COVID-19 group, the phylum Firmicutes showed a significant increase. Further, there were clear differences in relative abundance of several bacterial genera in contrast with the pre-infection group, including Streptococcus, Gemella, Granulicatella, Capnocytophaga, Leptotrichia, Fusobacterium, and Prevotella. We identified Gemella enrichment in the post-COVID-19 group, potentially serving as a recovery period performance indicator. Functional prediction revealed lipopolysaccharide biosynthesis downregulation in the post-COVID-19 group, an outcome with host inflammatory response modulation and innate defence mechanism implications. Conclusion: During the recovery phase of COVID-19, the oral microbiome diversity of front-line healthcare workers failed to fully return to its pre-infection state. Despite the negative COVID-19 test result one month later, notable disparities persisted in the composition and functional attributes of the oral microbiota.

Performance characteristics of "lollipop" swabs for the diagnosis of infection with SARS-CoV-2.

BACKGROUND: Common biologic samples used to diagnose COVID-19 include nasopharyngeal, nasal, or oropharyngeal swabs, and salivary samples. The performance characteristics of a sucked "lollipop" swab to detect SARS-CoV-2 virus is assessed in four small sub-studies. METHODS: In each sub-study, a flocked swab was sucked for 20 s and submitted for PCR detection of SARS-CoV-2 virus. RESULTS: Across all studies, 52 of 69 (75.4%) COVID-19 positive participants had positive "lollipop" swabs. Twelve of the 17 COVID-19 positive participants with negative "lollipop" swabs had known corresponding cycle threshold values of >37 from their nasal/nasopharyngeal swabs, an indication of low viral load at time of sampling. In a paired samples sub-study, the sensitivity and specificity of the "lollipop" swabs were 100% and 98%. CONCLUSIONS: "Lollipop" swabs performed satisfactorily especially in individuals with acute infection of COVID-19. "Lollipop" swabs are a simple method of sample collection for detecting SARS-CoV-2 virus and warrants additional consideration.

H9N2 influenza A viruses found to be enzootic in Punjab Pakistan's bird markets with evidence of human H9N2 nasal colonization.

OBJECTIVES: This study sought to detect and characterize influenza A (IAV) and influenza D (IDV) viruses circulating among commercial birds and shop owners in Pakistan's live bird markets. METHODS: Oropharyngeal swabs (n = 600; n = 300 pools) collected from poultry and nasopharyngeal swabs (n = 240) collected from poultry workers were studied for molecular evidence of IAV and IDV using real-time and conventional real-time reverse transcription polymerase chain reaction protocols. RESULTS: Nineteen (6.3%) poultry pools were positive for IAV and 73.9% of these were positive for H9N2 subtypes. Two (0.83%) poultry workers had evidence of IAV, and both were also H9N2 subtypes. The poultry and human IAV-positive specimens all clustered phylogenetically by Sanger and next-generation sequencing with previously detected H9N2 poultry isolates. No field specimens were positive for IDV. CONCLUSION: H9N2 IAV is likely enzootic in Punjab Province Pakistan's live bird markets and may be colonizing the noses of workers and market visitors. Regular monitoring for avian influenza-associated human illness in Punjab seems to be a needed public measure.

Longitudinal viral shedding and antibody response characteristics of men with acute infection of monkeypox virus: a prospective cohort study.

Understanding of infection dynamics is important for public health measures against monkeypox virus (MPXV) infection. Herein, samples from multiple body sites and environmental fomites of 77 acute MPXV infections (HIV co-infection: N = 42) were collected every two to three days and used for detection of MPXV DNA, surface protein specific antibodies and neutralizing titers. Skin lesions show 100% positivity rate of MPXV DNA, followed by rectum (88.16%), saliva (83.78%) and oropharynx (78.95%). Positivity rate of oropharynx decreases rapidly after 7 days post symptom onset (d.p.o), while the rectum and saliva maintain a positivity rate similar to skin lesions. Viral dynamics are similar among skin lesions, saliva and oropharynx, with a peak at about 6 d.p.o. In contrast, viral levels in the rectum peak at the beginning of symptom onset and decrease rapidly thereafter. 52.66% of environmental fomite swabs are positive for MPXV DNA, with highest positivity rate (69.89%) from air-conditioning air outlets. High seropositivity against A29L (100%) and H3L (94.74%) are detected, while a correlation between IgG endpoint titers and neutralizing titers is only found for A29L. Most indexes are similar between HIV and Non-HIV participants, while HIV and rectitis are associated with higher viral loads in rectum.

COVID-19: a meta-analysis of diagnostic test accuracy of commercial assays registered in Brazil

ABSTRACT The accuracy of commercially available tests for COVID-19 in Brazil remains unclear. We aimed to perform a meta-analysis to describe the accuracy of available tests to detect COVID-19 in Brazil. We searched at the Brazilian Health Regulatory Agency (ANVISA) online platform to describe the pooled sensitivity (Se), specificity (Sp), diagnostic odds ratio (DOR) and summary receiver operating characteristic curves (SROC) for detection of IgM/IgG antibodies and for tests using naso/oropharyngeal swabs in the random-effects models. We identified 16 tests registered, mostly rapid-tests. Pooled diagnostic accuracy measures [95%CI] were: (i) for IgM antibodies Se = 82% [76-87]; Sp = 97% [96-98]; DOR = 168 [92-305] and SROC = 0.98 [0.96-0.99]; (ii) for IgG antibodies Se = 97% [90-99]; Sp = 98% [97-99]; DOR = 1994 [385-10334] and SROC = 0.99 [0.98-1.00]; and (iii) for detection of SARS-CoV-2 by antigen or molecular assays in naso/oropharyngeal swabs Se = 97% [85-99]; Sp = 99% [77-100]; DOR = 2649 [30-233056] and SROC = 0.99 [0.98-1.00]. These tests can be helpful for emergency testing during the COVID-19 pandemic in Brazil. However, it is important to highlight the high rate of false negative results from tests which detect SARS-CoV-2 IgM antibodies in the initial course of the disease and the scarce evidence-based validation results published in Brazil. Future studies addressing the diagnostic performance of tests for COVID-19 in the Brazilian population are urgently needed.

Higher prevalence and gene amplification of HPV16 in oropharynx as compared to oral cavity

ABSTRACT Objective The objective of this study was to clarify differences regarding HPV16 infection and gene amplification between the oral cavity and oropharynx in healthy individuals. Material and Methods The subjects were 94 healthy asymptomatic individuals (41 males, 53 females; mean age 58.6 years, range 16-97 years) who visited the Department of Oral and Maxillofacial Reconstructive Surgery of the Hiroshima University Hospital from 2014 to 2015. Oral epithelial cells were collected from oral rinse and pharynx gargle samples and placed in saline. The human endogenous retrovirus gene ERV3-1 was used as a reference to estimate the number of human cells in each sample. DNA samples were extracted from approximately 10,000 human cells and tested for HPV16 DNA by PCR using a type-specific primer. Similarly, we analyzed the HPV16 viral copy number in HPV16-positive cases using real-time PCR to examine genomic amplification. Results The percentage of HPV16-positive cases was higher in the gargle (28.7%) as compared to the rinse (16.0%) samples. In the oral rinse samples, males (26.8%) showed a significantly higher rate of HPV16 than females (7.5%) (P=0.021). Importantly, in older subjects (aged 60-89 years), gargle samples showed a significantly higher rate of HPV16 (33.3%) than oral rinse samples (13.7%) (P=0.034). The average number of viral copies was approximately 8 times higher in the gargle than in the oral rinse samples (0.16±0.27 vs. 1.35±1.26 copy numbers per cell), a significant difference (P<0.001). Conclusion Our findings suggest that the oropharynx is more susceptible to HPV16 infection as compared to the oral cavity, while HPV16 gene amplification is also more commonly found in the oropharynx.

Polyphasic characterisation of Burkholderia cepaciacomplex species isolated from children with cystic fibrosis

Cystic fibrosis (CF) patients with Burkholderia cepacia complex (Bcc) pulmonary infections have high morbidity and mortality. The aim of this study was to compare different methods for identification of Bcc species isolated from paediatric CF patients. Oropharyngeal swabs from children with CF were used to obtain isolates of Bcc samples to evaluate six different tests for strain identification. Conventional (CPT) and automatised (APT) phenotypic tests, polymerase chain reaction (PCR)-recA, restriction fragment length polymorphism-recA, recAsequencing, and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) were applied. Bacterial isolates were also tested for antimicrobial susceptibility. PCR-recA analysis showed that 36 out of the 54 isolates were Bcc. Kappa index data indicated almost perfect agreement between CPT and APT, CPT and PCR-recA, and APT and PCR-recA to identify Bcc, and MALDI-TOF and recAsequencing to identify Bcc species. The recAsequencing data and the MALDI-TOF data agreed in 97.2% of the isolates. Based on recA sequencing, the most common species identified were Burkholderia cenocepacia IIIA (33.4%),Burkholderia vietnamiensis (30.6%), B. cenocepaciaIIIB (27.8%), Burkholderia multivorans (5.5%), and B. cepacia (2.7%). MALDI-TOF proved to be a useful tool for identification of Bcc species obtained from CF patients, although it was not able to identify B. cenocepacia subtypes.

Viscerotropic velogenic Newcastle disease virus replication in feathers of infected chickens

Newcastle disease viruses (NDVs) cause systemic diseases in chickens with high mortality. However, little is known about persistence of NDVs in contaminated tissues from infected birds. In this study, we examined viral replication in the feather pulp of chickens inoculated with viscerotropic velogenic NDV (vvNDV) genotype VII. Reverse transcription real-time PCR and immunohistochemistry were used to investigate viral persistence in the samples. vvNDV was detected in the oropharynx and cloaca and viral antigens were detected in the feathers, suggesting that feathers act as sources of viral transmission.

Comparative study between biopsy and brushing sampling methods for detection of human papillomavirus in oral and oropharyngeal cavity lesions, / Estudo comparativo entre biópsia e escovado na pesquisa do papilomavírus humano em lesões de cavidade oral e de orofaringe

ABSTRACT INTRODUCTION: Many epidemiological studies have suggested that human papillomavirus (HPV), especially type 16, is involved in the genesis of squamous cell carcinoma of the oral cavity and oropharynx, especially in young, non-smoking patients; thus, its detection in lesions in this region is important. OBJECTIVE: To clarify the capacity of the brushing sampling method to detect the presence of HPV in oral or oropharyngeal lesions through polymerase chain reaction (PCR) testing, and to compare the results with those obtained by biopsy. METHODS: Prospective study of adult patients with oral or oropharyngeal lesions assessed by PCR, comparing biopsy specimens with samples obtained by the brushing method. The study was approved by the Research Ethics Committee of the institution. RESULTS: A total of 35 sample pairs were analyzed, but 45.7% of the brushing samples were inadequate (16/35) and, thus, only 19 pairs could be compared. There was agreement of results in 94.7% (18/19) of the pairs, with HPV identified in 16 of them. HPV DNA was detected in 8.6% (3/35) of biopsy and 5.7% (2/35) of brushing samples. CONCLUSION: There was no statistically significant difference between the two methods, but the brushing sampling method showed a higher number of inadequate samples, suggesting that it is an unreliable method for surveillance.

Resumo INTRODUÇÃO: Muitos estudos epidemiológicos indicam a participação do papilomavírus humano, especialmente o tipo 16, na carcinogênese dos tumores espinocelulares das cavidade oral e oro-faríngea, principalmente em jovens e não fumantes, sendo portanto importante sua detecção nas lesões desta região. OBJETIVO: Elucidar a habilidade do escovado em detectar o papilomavírus humano, pela reação em cadeia da polimerase, nas lesões orais e orofaríngeas, comparando os resultados com os obtidos por biópsia. MÉTODO: Estudo prospectivo de pacientes com lesões orais e orofaríngeas, pela reação em cadeia da polimerase, no qual foram pareados os resultados de amostras obtidas por escovado e por biópsia. A pesquisa foi aprovada pelo Comitê de Ética em Pesquisa da instituição. RESULTADO: Foram analisados 35 pares de amostras, porém estavam inapropriadas para análise 45,7% (16/35) das amostras obtidas por escovado, e portanto, somente 19 pares puderam ser comparados. Em 94,7% dos pares houve concordância dos resultados, sendo encontrado o papilomavírus humano − 16 em um destes pares. O ácido desoxirribonucleico do papilomavírus humano foi detectado em 8,6% (3/35) das biópsias e em 5,7% (2/35) dos escovados. CONCLUSÃO: Não houve diferença estatística entre os métodos, mas como houve um grande número de amostras obtidas por escovado inapropriadas, este parece não ser confiável para o rastreamento.

Determinacao da prevalencia de HPV em amostras de mucosa oral/orofaringea em um distrito rural de Sao Paulo / Determination of HPV prevalence in oral/oropharyngeal mucosa samples in a rural district of Sao Paulo

OBJETIVO: Averiguar a eficácia da metodologia para coleta de amostras em cavidade oral e orofaringe e determinar a prevalência do HPV na cavidade oral e orofaringe de adultos e crianças. MÉTODO: A população estudada foi atendida por um programa assistencial em um distrito rural de São Paulo. Os indivíduos foram convidados a doar amostras independentemente de queixas. RESULTADOS E CONCLUSÃO: Foram incluídos no estudo 47 homens, 77 mulheres e 22 crianças, dos quais amostras da cavidade oral foram obtidas por bochecho e gargarejo com antisséptico oral comercial. Foram encontrados três resultados positivos (2,4%) em adultos, duas amostras de HPV 55 e uma amostra de HPV 58. Não foram observados resultados positivos em crianças. Além disso, concluímos que o método de coleta com o enxágue bucal com antisséptico mostrou-se eficaz e rápido para a detecção de HPV na cavidade oral e orofaríngea na população geral. .

Knowledge about HPV infection in the oral cavity/oropharynx may contribute to the elucidation of the role it plays in Head and Neck Squamous Cell Carcinoma (HNSCC). OBJECTIVE: To determine the effectiveness of the methodology used for sampling the oral cavity and oropharynx mucosae and to determine the prevalence of HPV in the oral cavity and oropharynx of adults and children. METHOD: The study population was served by an assistance program in a rural district of São Paulo. The subjects were asked to donate samples regardless of complaints. RESULTS AND CONCLUSION: The study included 47 men, 77 women and 22 children, of which the oral cavity samples were obtained by gargling with commercially-available antiseptic mouthwash. We found 3 positive samples (2.4%) in adults: 2 HPV 55 and one HPV 58. No positive results were found in children. Furthermore we concluded that the sampling method with the mouthwash proved effective and fast for the detection of HPV in the oral cavity and oropharynx in the general population. .

Prolonged excretion of a low-pathogenicity H5N2 avian influenza virus strain in the Pekin duck

H5N2 strains of low-pathogenicity avian influenza virus (LPAIV) have been circulating for at least 17 years in some Mexican chicken farms. We measured the rate and duration of viral excretion from Pekin ducks that were experimentally inoculated with an H5N2 LPAIV that causes death in embryonated chicken eggs (A/chicken/Mexico/2007). Leghorn chickens were used as susceptible host controls. The degree of viral excretion was evaluated with real-time reverse transcriptase-polymerase chain reaction (RRT-PCR) using samples from oropharyngeal and cloacal swabs. We observed prolonged excretion from both species of birds lasting for at least 21 days. Prolonged excretion of LPAIV A/chicken/Mexico/2007 is atypical.

Avaliaçäo citológica da orofaringe de mulheres portadoras do HPV genital / Cytological evaluation of the oropharynge in carriers women of genital HPV

O Vírus do Papiloma Humano (HPV) na mucosa oral das mulheres com lesoes clínicas ou subclínicas do condiloma nos órgaos genitais foi pesquisado através de esfregaço citológico da cavidade bucal. Para a análise, empregou-se coloraçao de Papanicolaou e técnica de imunoperoxidase. A casuística constou de 51 pacientes com diagnóstico clínico e histológico de HPV genital, atendidas no período de agosto de 1994 a julho de 1995. A idade média das pacientes foi de 22,5 anos, sendo que a média das idades na primeira relaçao foi de 17,4 anos. Destas mulheres, 60 por cento tiveram mais que três parceiros sexuais na vida, e a prática do sexo oral foi relatada em 45 por cento dos casos. O sexo anal, apesar da dificuldade em sua abordagem, foi relatado em 35 por cento dos casos. As lesoes genitais com HPV apresentaram-se nas formas clínicas e subclínicas em 86 por cento e l4 por cento dos casos, respectivamente: na vulva, 53 por cento; no colo, 14 por cento; na vagina, 6 por cento e mais de um local, 27 por cento. No nível de orofaringe, sinais citológicos como discariose, binucleaçao, paraceratose foram interpretados como suspeitos da presença do HPV, ocorrendo em 65 por cento dos casos. Evidências conclusivas desta infecçao estiveram presentes em 6 por cento dos casos analisados e, em 29 por cento das vezes, nao houve qualquer suspeita ou evidência citológica do HPV na mucosa orofaríngea. A paciente com lesao clínica de HPV genital apresentou evidência ou suspeita de HPV oral mais freqüente que as pacientes com lesao subclínica. O estudo serviu para mostrar que o vírus do papiloma humano pode estar presente na orofaringe de mulheres portadoras de HPV genital, mesmo nao havendo lesoes clinicamente detectáveis na mucosa oral.