Human virome in nasopharynx and tracheal secretion samples

BACKGROUND In Brazil the implementation of the Sentinel Surveillance System of Influenza began in 2000. Central public health laboratories use reverse transcription-quantitative polymerase chain reaction (RT-qPCR) for diagnosis of respiratory viruses, but this protocol identifies only specific targets, resulted in inconclusive diagnosis for many samples. Thus, high-throughput sequencing (HTS) would be complementary method in the identification of pathogens in inconclusive samples for RT-qPCR or other specific detection protocols. OBJECTIVES This study aimed to detect unidentified viruses using HTS approach in negative samples of nasopharynx/tracheal secretions by the standard RT-qPCR collected in the Federal District, Brazil. METHODS Nucleic acids were extracted from samples collected in winter period of 2016 and subjected to HTS. The results were confirmed by the multiplex PR21 RT-qPCR, which identifies 21 respiratory pathogens. FINDINGS The main viruses identified by HTS were of families Herpesviridae, Coronaviridae, Parvoviridae and Picornaviridae, with the emphasis on rhinoviruses. The presence of respiratory viruses in the samples was confirmed by the PR21 multiplex RT-qPCR. Coronavirus, enterovirus, bocavirus and rhinovirus were found by multiplex RT-qPCR as well as by HTS analyses. MAIN CONCLUSIONS Wide virus diversity was found by different methodologies and high frequency of rhinovirus occurrence was confirmed in population in winter, showing its relevance for public health.

Malignant Catarrhal Fever in Brazilian cattle presenting with neurological syndrome

Abstract Malignant Catarrhal Fever (MCF) was investigated in the central nervous system of cattle with neurological syndrome. Two-hundred-ninety samples were analyzed by histology, and molecular methods to detect ovine herpesvirus type 2 (OvHV-2) were optimized and validated. The qualitative polymerase chain reaction (qualitative PCR) analytical sensitivity was 101 DNA copies/µL and found 4.8% (14/290) positive for OvHV-2. The quantitative polymerase chain reaction (qPCR) analytical sensitivity was 100 DNA copy/µL and 5.9% (17/290) positivity, with 47.1% (8/17) of the positive samples presenting histological evidence of non-purulent meningo-encephalitis. The qualitative PCR products (422 bp of the ORF75 region) were sequenced and submitted to phylogenetic analysis. Identity matrices showed 100% similarity in OvHV-2 samples obtained in this study and those recovered from GenBank, corroborating other studies.

Genotypic characterization of psittacid herpesvirus isolates from Brazil

Abstract Thirty-six isolates of psittacid herpesvirus (PsHV), obtained from 12 different species of psittacids in Brazil, were genotypically characterized by restriction fragment length polymorphism (RFLP) analysis and PCR amplification. RFLP analysis with the PstI enzyme revealed four distinct restriction patterns (A1, X, W and Y), of which only A1 (corresponding to PsHV-1) had previously been described. To study PCR amplification patterns, six pairs of primers were used. Using this method, six variants were identified, of which, variants 10, 8, and 9 (in this order) were most prevalent, followed by variants 1, 4, and 5. It was not possible to correlate the PCR and RFLP patterns. Twenty-nine of the 36 isolates were shown to contain a 419 bp fragment of the UL16 gene, displaying high similarity to the PsHV-1 sequences available in GenBank. Comparison of the results with the literature data suggests that the 36 Brazilian isolates from this study belong to genotype 1 and serotype 1.

Herpes viruses and human papilloma virus in nasal polyposis and controls / Herpesvírus e vírus do papiloma humano na polipose nasal e controles

ABSTRACT INTRODUCTION: Chronic rhinosinusitis with nasal polyps is a multifactorial disease entity with an unclear pathogenesis. Contradictory data exist in the literature on the potential implication of viral elements in adult patients with chronic rhinosinusitis. OBJECTIVE: To compare the prevalence of human herpes viruses (1-6) and Human Papilloma Virus in adult patients with chronic rhinosinusitis with nasal polyps and healthy controls. METHODS: Viral DNA presence was evaluated by real-time polymerase chain reaction application to nasal polyps specimens from 91 chronic rhinosinusitis with nasal polyps patients and nasal turbinate mucosa from 38 healthy controls. RESULTS: Epstein-Barr virus positivity was higher in nasal polyps (24/91; 26.4%) versus controls (4/38; 10.5%), but the difference did not reach significance (p = 0.06). Human herpes virus-6 positivity was lower in nasal polyps (13/91; 14.29%) versus controls (10/38; 26.32%,p = 0.13). In chronic rhinosinusitis with nasal polyps group, 1 sample was herpes simplex virus-1-positive (1/91; 1.1%), and another was cytomegalovirus-positive (1/91; 1.1%), versus none in controls. No sample was positive for herpes simplex virus-2, varicella-zoster virus, high-risk-human papilloma viruses (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59) and low-risk-human papilloma viruses (6, 11). CONCLUSION: Differences in Epstein-Barr virus and human herpes virus-6 positivity among patients with chronic rhinosinusitis with nasal polyps and healthy controls are not statistically significant, weakening the likelihood of their implication in chronic rhinosinusitis with nasal polyps pathogenesis.

RESUMO INTRODUÇÃO: A rinossinusite crônica com pólipos é uma doença multifatorial de etiopatogênese ainda não definida. Existem dados contraditórios na literatura sobre a implicação potencial de elementos virais na etiologia de pólipos nasossinusais. OBJETIVO: Comparar a prevalência de herpes vírus humanos (1-6) e papiloma vírus humano em pacientes adultos com rinossinusite crônica com pólipos nasais (CRwNP) e controles saudáveis. MÉTODO: A presença de DNA viral foi avaliada por PCR em tempo real, em amostras de pólipos nasais de 91 pacientes com CRwNP e na mucosa das conchas nasais de 38 controles saudáveis. RESULTADOS: A positividade do EBV foi maior nos pólipos nasais (24/91; 26,4%) do que nos controles (4/38; 10,5%), mas a diferença não foi significante (p = 0,06). O HHV-6 apresentou positividade menor nos pólipos nasais (13/91; 14,29%) do que os controles (10/38; 26,32%), (p = 0,13). No grupo CRwNP, uma amostra foi positiva para o vírus herpes simples (HSV-1) (1/91; 1,1%), e uma para citomegalovírus (CMV) (1/91; 1,1%); e nenhuma amostra foi positiva no grupo controle. Não houve amostra positiva para HSV-2, VZV, HR-HPV (16,18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59) e LR-HPV (6,11). CONCLUSÃO: Diferenças de positividade do EBV e HHV-6 entre pacientes com CRwNP e controles saudáveis não são estatisticamente significantes, enfraquecendo a probabilidade de sua implicação na patogênese da CRwNP.

Lack of associaiion between herpesvirus detectin in saliva and gingivitis in hhiv‑infected children / Ausência de associação entre a detecção de herpesvírus na saliva e gengivite em crianças infectadas pelo HIV

The aims of this study were to compare the detection of human herpesviruses (HHVs) in the saliva of HIV-infected and healthy control children, and to evaluate associations between viral infection and gingivitis and immunodeficiency. Saliva samples were collected from 48 HIV-infected and 48 healthy control children. Clinical and laboratory data were collected during dental visits and from medical records. A trained dentist determined gingival indices and extension of gingivitis. Saliva samples were tested for herpes simplex virus types 1 and 2 (HSV-1 and HSV-2), varicella zoster virus (VZV), Epstein-Barr virus (EBV), and cytomegalovirus (CMV) by nested polymerase chain reaction assays. Thirty-five HIV-infected and 16 control children had gingivitis. Seventeen (35.4%) HIV-infected children and 13 (27%) control children were positive for HHVs. CMV was the most commonly detected HHV in both groups (HIV-infected, 25%; control, 12.5%), followed by HSV-1 (6.2% in both groups) and HSV-2 (HIV-infected, 4.2%; control, 8.3%). The presence of HHVs in saliva was not associated with the presence of gingivitis in HIV-1-infected children (p = 0.104) or healthy control children (p = 0.251), or with immunosuppression in HIV-infected individuals (p = 0.447). Gingivitis was correlated with HIV infection (p = 0.0001). These results suggest that asymptomatic salivary detection of HHVs is common in HIV-infected and healthy children, and that it is not associated with gingivitis.

Os objetivos deste estudo foram detectar a presença de herpesvírus humanos (HHVs) na saliva de crianças infectadas pelo HIV, em comparação com controles saudáveis e avaliar a associação entre infecção viral, gengivite e imunodeficiência. Para este fim, foram colhidas amostras de saliva de 48 crianças HIV-positivas e 48 controles saudáveis. O índice gengival e extensão de gengivite foram determinados por um dentista treinado. Informações clínicas e laboratoriais foram obtidas durante a consulta odontológica e dos registros médicos. As amostras de saliva foram testadas para detecção de vírus herpes simplex tipos 1 e 2 (HSV-1 e HSV-2), vírus da varicela-zoster (VVZ), vírus Epistein-Barr (EBV) e citomegalovírus (CMV) através de nested-PCR. Trinta e cinco crianças HIV-positivas e 16 crianças do grupo controle apresentavam gengivite. Dezessete (35,4%) crianças HIV-positivas e 13 (27%) crianças controle testaram positivo para a presença de HHVs. CMV foi o vírus mais comum detectado em ambos os grupos (25% HIV-positivas e 12,5% de controle), seguido por HSV-1 (6,2% de ambos os grupos) e HSV-2 (4,2% HIV-positivas e 8,3% de controle). Não houve associação entre a detecção de HHVs na saliva e a presença de gengivite em ciranças HIV-positivas (p = 0.104) ou crianças saudáveis (p = 0,251), ou com imunossupressão em indivíduos HIV-positivos (p = 0,447). Foi observada uma correlação entre a infecção por HIV e a presença de gengivite (p = 0,0001). Os resultados sugerem que a detecção salivar assintomática de HHVs é comum entre crianças HIV-positivas e crianças saudáveis, e não está associada à gengivite.

Current status of herpesvirus identification in the oral cavity of HIV-infected children

INTRODUCTION: Some viruses of the Herpesviridae family are frequently the etiologic agents of oral lesions associated with HIV. The aim of this study was to identify the presence of herpes simplex virus types 1 and 2 (HSV-1, HSV-2), Varicella Zoster virus (VZV), Epstein-Barr virus (EBV), human cytomegalovirus (HCMV), human herpesvirus type 6, type 7 and type 8 (HHV-6, HHV-7 and HHV-8) in the oral cavity of HIV-infected children/adolescents and verify the association between viral subtypes and clinical factors. METHODS: The cells of oral mucosa were collected from 50 HIV infected children/adolescents, 3-13 years old (mean age 8.66). The majority (66%) of selected were girls, and they were all outpatients at the pediatric AIDS clinic of a public hospital in Rio de Janeiro. Nested-PCR was used to identify the viral types. RESULTS: Absence of immunosuppression was observed in 66% of the children. Highly active antiretroviral therapy (HAART) was used by 72.1% of selected and moderate viral load was observed in 56% of the children/adolescents. Viral types were found in 86% of the children and the subtypes were: HSV-1 (4%), HSV-2 (2%), VZV (4%), EBV (0%), HCMV (24%), HHV6 (18%), HHV-7 (68%), HHV8 (0%). CONCLUSIONS: The use of HAART has helped to reduce oral lesions, especially with herpes virus infections. The health professionals who work with these patients should be aware of such lesions because of their predictive value and the herpes virus can be found circulating in the oral cavity without causing lesions.

PCR detection of multiple human herpesvirus DNA in saliva from HIV-infected individuals in Teresina, State of Piauí, Brazil / Detecção por PCR do DNA de vários herpesvírus humanos na saliva de indivíduos infectados pelo HIV em Teresina, Estado do Piauí, Brasil

INTRODUCTION: Human herpesviruses are frequently associated with orofacial diseases in humans (HSV-1, EBV, CMV and HHV-8), some can also cause systemic disease (CMV and HHV-8). The transmission of these viruses occurs by contact with infected secretions, especially saliva. Human immunodeficiency virus infection is associated with an increased risk of HHVs and related diseases. METHODS: This work aimed to detect HSV-1, EBV, CMV and HHV-8 DNA in saliva of HIV-infected patients from Teresina, northeast Brazil, by PCR and compare these findings with age and sex matched HIV-seronegative individuals. RESULTS: No difference in prevalence was verified between HHV detection in the saliva of HIV-seropositive individuals and controls. The individual frequencies of these viruses in these two populations were different. HIV seropositivity correlated positively with the presence of CMV (OR: 18.2, p= 0.00032) and EBV (OR: 3.44, p= 0.0081). No association between CD4 counts and the prevalence of HHVs in the saliva was observed; however, a strong association was determined between seropositivity and the presence of multiple HHV DNAs in saliva (OR: 4.83, p = 0.0028). CONCLUSIONS: These findings suggest the asymptomatic salivary shedding of HHVs is a common event between HIV-seropositive and seronegative individuals from Teresina, Piauí, Brazil, and, especially for HIV-seropositive patients, saliva is a risk factor for the acquisition/transmission of multiple HHVs.

INTRODUÇÃO: Alguns herpesvírus humanos são frequentemente associados a doenças orofaciais em humanos. A transmissão destes vírus ocorre através do contato com secreções contaminadas, especialmente a saliva. A infecção pelo vírus da imunodeficiência humana é considerada um fator de risco para a aquisição de HHVs e doenças correlatas. MÉTODOS: Este trabalho teve como objetivo detectar por PCR o DNA de HSV-1, EBV, CMV e HHV-8 na saliva de pacientes infectados com HIV em Teresina, nordeste do Brasil, e comparar os dados obtidos com o grupo controle (indivíduos HIV negativos). RESULTADOS: Não há diferença na prevalência de detecção de HHVs na saliva de indivíduos HIV soropositivos e soronegativos. No entanto, as frequências individuais de detecção dos diferentes HHVs são diferentes entre estas duas populações. A soropositividade para HIV apresentou correlação positiva com a presença de CMV (OR: 18,2, p = 0,00032) e EBV (OR: 3,44, p = 0,0081). Não foi verificada nenhuma associação entre a contagem de CD4 e prevalência de HHVs na saliva, no entanto existe uma forte associação entre a soropositividade e a detecção do DNA de vários HHVs na saliva (OR: 4,83, p = 0,0028). CONCLUSÕES: Estes resultados sugerem que a transmissão salivar de HHVs é um evento comum entre os indivíduos HIV soropositivos e soronegativos de Teresina, Piauí, Brasil, e, especialmente para os pacientes soropositivos, a saliva é um fator de risco para a aquisição/transmissão de múltiplos HHVs.

Design of degenerate primers for multiplex nested-PCR detection of human lymphotropic herpesviruses.

To develop the rapid diagnosis and typing of human lymphotropic herpesviruses by using multiplex nested-PCR, the primary PCR (1(o) PCR) primers were redesigned as degenerate primers based on a highly conserved sequences of each DNA polymerase gene of EBV, CMV, HHV-6, HHV-7 and HHV-8. The forward degenerate primer (HHV/1+) contained 12 different sequences, whereas there were 8 different sequences in the reverse degenerate primer (HHV/ 1-). Optimization of multiplex nested-PCR assay conditions were performed to search for the appropriate amount of degenerate primers, dNTP, Taq DNA polymerase, template of secondary PCR (2(o) PCR) and annealing temperature used in 1(o) PCR reaction. Detection sensitivity was the same as described in previous report (approximately 10-100 genome copies). To ensure a true negative result, PCR detection of hepatitis B virus genome was used as internal control. Our presented results, the designed degenerate primers could be used to detect various types of HHV by multiplex nested-PCR.

Os herpesvírus humanos no curso da síndrome da imunodeficiência adquirida / The human herpesvirus in curse of acquired immunodeficiency syndrome

As infecçöes provocadas pelos herpesvírus humanos formam um grupo de moléstias de distribuiçäo ubíqua. Nos pacientes imunodeprimidos, em especial nos HIV positivos, a infecçäo provocada pelos herpesvírus é causa importante de morbidade e mortalidade. Essas moléstias podem recorrer com mais freqüência e com curso mais grave e prolongado. Graças à grande carga viral existente, säo também mais propensos a desenvolver resistência às drogas antivirais. Säo discutidas as características mais relevantes da infecçäo pelos herpesvírus nos imunocomprometidos com especial ênfase em herpes simples, herpes-zóster, mononucleose e infecçäo peloCMV, HHV-6, HHV-7,e HHV-8.