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.