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1.
Washington; Organización Panamericana de la Salud; mar. 24, 2021. 9 p.
Non-conventional in Spanish | LILACS | ID: biblio-1151432

ABSTRACT

A la fecha, 141 los países/territorios han detectado casos de infección por alguna de las tres variantes de preocupación (VOC) reconocidas actualmente por la Organización Mundial de la Salud (OMS). De ese total, 32 países/territorios corresponden a la Región de las Américas.


Subject(s)
Pneumonia, Viral/genetics , DNA, Viral/genetics , Coronavirus Infections/genetics , Pandemics/prevention & control , Epidemiological Monitoring , Betacoronavirus/immunology , Mutation , Americas/epidemiology
2.
Arq. neuropsiquiatr ; 78(3): 163-168, Mar. 2020. tab
Article in English | LILACS | ID: biblio-1098075

ABSTRACT

Abstract Herpes simplex virus (HSV) is a cause of a severe disease of the central nervous system (CNS) in humans. The demonstration of specific antibodies in the cerebrospinal fluid (CSF) may contribute to the retrospective neurological diagnosis. However, the commercial immunological tests for HSV infection are for use in serum samples. Objective: The aim of the present study was to adapt a commercial kit anti-HSV IgG used for serum samples to be performed with a CSF sample. Methods: Forty CSF specimens from 38 patients with suspected CNS HSV infection were serially diluted for detecting anti-HSV IgG by enzyme immunoassay (EIA). The same samples were also analyzed with the polymerase chain reaction (PCR). Results: The sensitivity of EIA test for HSV was 5% (dilution 1:40) and 65% (dilution 1:2) in CSF, and HSV DNA PCR was 15%. The combined analysis of EIA (dilution 1:2) and PCR increased the sensitivity up to 72.5%. The inflammatory CSF was associated with positive HSV PCR. Conclusions: We demonstrated the importance to adapt serological anti-HSV IgG EIA test for CSF assays to increase the accuracy of the analysis, considering the low concentration of specific antibodies in CSF.


Resumo O vírus herpes simples (HSV) é um dos agentes causadores de uma doença grave no sistema nervoso central (SNC) em humanos. A detecção de anticorpos específicos no líquido cefalorraquidiano (LCR) pode contribuir para o diagnóstico neurológico retrospectivo. Entretanto, os testes imunológicos comerciais são para uso em amostras de soro. Objetivo: Adaptar um kit comercial sorológico anti-HSV IgG para ser utilizado no de LCR. Metodos: Quarenta amostras de LCR de 38 pacientes com suspeita de infecção por HSV no SNC foram diluídas pesquisa de anticorpos anti-HSV IgG pelo método imunoenzimático (EIA). Além disso, as mesmas amostras também foram analisadas por reação em cadeia da polimerase (PCR). Resultados: A sensibilidade do teste EIA para o HSV consistiu em 5% (diluição 1:40) e 65% (diluição 1:2) no LCR, e o PCR do DNA do HSV, 15%. A análise combinada de EIA (diluição 1:2) e PCR aumentou a sensibilidade para 72,5%. Houve associação entre presença do LCR inflamatório e PCR positiva para HSV. Conclusões: Demonstramos a importância na adaptação previa do teste sorológico anti-HSV IgG EIA para ensaios do no LCR, a fim de aumentar a acuracia da análise, considerando a baixa concentração de anticorpos específicos no LCR.


Subject(s)
Humans , Male , Female , Adult , Middle Aged , Cerebrospinal Fluid/virology , Simplexvirus/isolation & purification , Herpes Simplex/diagnosis , Herpes Simplex/virology , Antibodies, Viral/cerebrospinal fluid , Viral Proteins , DNA, Viral/genetics , Polymerase Chain Reaction/methods , Retrospective Studies , Simplexvirus/genetics , DNA-Directed DNA Polymerase/genetics , Exodeoxyribonucleases , Herpes Simplex/cerebrospinal fluid , Nervous System
3.
National Journal of Andrology ; (12): 906-910, 2020.
Article in Chinese | WPRIM | ID: wpr-880290

ABSTRACT

Objective@#To investigate the distribution of the gene subtypes of human papillomavirus (HPV) in male patients with condyloma acuminatum (CA) and analyze the characteristics of the gene subtypes.@*METHODS@#We extracted genomic DNA of the HPV virus from the genital tissue of 70 male CA patients, detected the DNA subtypes of HPV using the PCR-reverse dot hybridization technique, and analyzed the rates of different subtypes identified and their characteristics of distribution in different age groups.@*RESULTS@#The male HPV-positive patients were mainly infected at the age of 20-39 years, primarily with high- and low-risk mixed infection of various subtypes, which accounted for 61.54% in the 20- to 29-year-olds and 42.86% in the 30- to 39-year-olds. Among the 70 CA patients, 22 HPV subtypes were identified, the top five subtypes including HPV 11 (21.08%), HPV 6 (19.46%), HPV 42 (6.49%), HPV 59 (6.49%) and HPV 53 (5.95%); 20 infected with a single subtype (28.57%), 19 with two subtypes (27.14%) and 31 with three or more (44.29%); and 30 infected with a low-risk single subtype (42.86%) and 40 with both high- and low-risk multiple subtypes (57.14%).@*CONCLUSIONS@#Male patients with CA are mainly infected with HPV 11 and HPV 6, with a significantly higher rate of multi-subtype than single-subtype infection, and the multi-subtype patients chiefly with high- and low-risk mixed infection. Men aged 20-39 years old are most commonly affected by CA.


Subject(s)
Adult , Condylomata Acuminata/virology , DNA, Viral/genetics , Genotype , Humans , Male , Papillomaviridae/genetics , Papillomavirus Infections/virology , Young Adult
4.
Article in Chinese | WPRIM | ID: wpr-879926

ABSTRACT

A large number of viruses have been found to be associated with ocular diseases, including human adenovirus, human herpesvirus (HHV), human T lymphotropic virus type-1 (HTLV-1), and newly emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This group of diseases is prone to be misdiagnosed or missed diagnosis, resulting in serious tissue and visual damage. Etiological diagnosis is a powerful auxiliary mean to diagnose the ocular diseases associated with human adenovirus, herpes simplex virus 1 and varicella-zoster virus, and it provides the leading diagnosis evidence of infections with herpes simplex virus 2, Epstein-Barr virus, cytomegalovirus, HHV-6/7, HHV-8, HTLV-1 and SARS-CoV-2. Virus isolation, immunoassay and genetic diagnosis are usually used for etiologic diagnosis. For genetic diagnosis, the PCR technique is the most important approach because of its advantages of rapid detection, convenient operation, high sensitivity and high specificity.


Subject(s)
COVID-19 , Coronavirus Infections/virology , DNA, Viral/genetics , Eye Diseases/virology , Humans , Pandemics , Pneumonia, Viral/virology , Research/trends , Virus Diseases/virology
5.
Mem. Inst. Oswaldo Cruz ; 114: e190198, 2019. tab, graf
Article in English | LILACS | ID: biblio-1040605

ABSTRACT

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.


Subject(s)
Humans , Parvoviridae/isolation & purification , Picornaviridae/isolation & purification , Trachea/virology , Nasopharynx/virology , Coronaviridae/isolation & purification , Herpesviridae/isolation & purification , Parvoviridae/classification , Parvoviridae/genetics , Picornaviridae/classification , Picornaviridae/genetics , DNA, Viral/genetics , RNA, Viral/genetics , Coronaviridae/classification , Coronaviridae/genetics , Reverse Transcriptase Polymerase Chain Reaction , Real-Time Polymerase Chain Reaction , Herpesviridae/classification , Herpesviridae/genetics
6.
Braz. j. microbiol ; 49(supl.1): 83-92, 2018. tab, graf
Article in English | LILACS | ID: biblio-974337

ABSTRACT

Abstract Small ruminant lentiviruses (SRLV) have high genetic variability which results in different viral strains around the world. This create a challenge to design sensible primers for molecular diagnosis in different regions. This work proposes a protocol of duplex nested-PCR for the precise diagnosis of SRLV. The technique was designed and tested with the control strains CAEV Co and MVV 1514. Then, field strains were submitted to the same protocol of duplex nested-PCR. Blood samples of sheep and goats were tested with AGID and nested PCR with specific primers for pol, gag and LTR. The AGID results showed low detection capacity of positive animals, while the nested PCR demonstrated a greater capacity of virus detection. Results demonstrated that LTR-PCR was more efficient in detecting positive sheep samples, whereas gag-PCR allowed a good detection of samples of positive goats and positive sheep. In addition, pol-PCR was more efficient with goat samples than for sheep. Duplex nested PCR performed with standard virus samples and field strains demonstrated that the technique is more efficient for the detection of multiple pro-viral DNA sequences. This study demonstrated a successful duplex nested PCR assay allowing a more accurate diagnosis of SRLV.


Subject(s)
Animals , Sheep Diseases/virology , Goat Diseases/virology , Polymerase Chain Reaction/methods , Lentivirus Infections/veterinary , Sheep Diseases/diagnosis , DNA, Viral/genetics , Goats , Sheep , Goat Diseases/diagnosis , Lentivirus Infections/diagnosis , Lentivirus Infections/virology , DNA Primers/genetics
7.
Clinics ; 73: e465, 2018. tab, graf
Article in English | LILACS | ID: biblio-974922

ABSTRACT

OBJECTIVE: The aim of this study is to investigate the presence of human papillomavirus DNA and genotypes in breast cancer and normal breast tissue samples obtained from women from the northeast region of Brazil. METHOD: One hundred three breast cancer samples and 95 normal breast samples, as the non-malignant controls, were studied. DNA extraction was verified by human beta-globin gene amplification, and polymerase chain reaction was conducted based on HPV L1-specific consensus primers MY09/MY11 and GP5+/GP6+, followed by nested multiplex polymerase chain reaction with type-specific primers for the E6/E7 consensus region. RESULTS: Human papillomavirus DNA was detected in 51 (49.5%) breast carcinoma samples and 15 (15.8%) normal breast samples (p<0.0001). Human papillomavirus genotypes 6 and 11 were identified in 15.2% of all samples. CONCLUSIONS: The high frequency of human papillomavirus infection in breast cancer samples indicates a potential role of this virus in breast carcinogenesis in the studied participants.


Subject(s)
Humans , Female , Adult , Middle Aged , Aged , Aged, 80 and over , Breast Neoplasms/virology , DNA, Viral/genetics , Papillomavirus Infections/genetics , Case-Control Studies , Polymerase Chain Reaction , Cross-Sectional Studies , Genotype
8.
Mem. Inst. Oswaldo Cruz ; 112(11): 790-792, Nov. 2017. graf
Article in English | LILACS | ID: biblio-1040563

ABSTRACT

Staphylococcus aureus subsp. aureus, commonly referred as S. aureus, is an important bacterial pathogen frequently involved in hospital- and community-acquired infections in humans, ranging from skin infections to more severe diseases such as pneumonia, bacteraemia, endocarditis, osteomyelitis, and disseminated infections. Here, we report the complete closed genome sequence of a community-acquired methicillin-resistant S. aureus strain, USA400-0051, which is a prototype of the USA400 clone.


Subject(s)
Humans , Staphylococcal Infections/virology , DNA, Viral/genetics , Genome, Bacterial/genetics , Methicillin-Resistant Staphylococcus aureus/genetics , Community-Acquired Infections/microbiology
9.
Braz. j. infect. dis ; 21(5): 525-529, Sept.-Oct. 2017. tab
Article in English | LILACS | ID: biblio-888904

ABSTRACT

Abstract Infection by hepatitis B virus (HBV) is a worldwide public health problem. Chronic HBV infection with high viral replication may lead to cirrhosis and/or hepatocellular carcinoma. Mutant HBV strains, such as the HBV A1762T/G1764A double mutant, have been associated with poor prognosis and higher risk of the patient for developing cirrhosis and/or hepatocellular carcinoma. This study analyzed the presence of the HBV A1762T/G1764A double mutant in patients with chronic HBV and its association with clinical parameters such as viral load, aminotransferases, and HBV antigens. A total of 49 patients with chronic hepatitis B were included in the study, and the HBV A1762T/G1764A double mutant strain was detected in four samples (8.16%) by polymerase chain reaction followed by restriction fragment length analysis (PCR-RFLP). The viral load was not significantly different between patients with or without the double mutant strain (p = 0.43). On the other hand, carriers of the HBV A1762T/G1764A double mutant had higher levels of ALT (p = 0.0028), while AST levels did not differ between groups (p = 0.051). In this study, 75% of the samples with the HBV A1762T/G1764A double mutation were HBeAg negative and anti-HBe positive, reflecting seroconversion even though they still displayed high viral loads. Our study has shown that the HBV A1762T/G1764A double mutant strain circulates in Brazilian patients, and is associated with elevated levels of ALT and HBeAg seroconversion.


Subject(s)
Humans , Male , Female , Adult , Middle Aged , Aged , Young Adult , DNA, Viral/genetics , Hepatitis B virus/genetics , Hepatitis B, Chronic/virology , Hepatitis B e Antigens/blood , Mutation/genetics , Brazil , Polymerase Chain Reaction , Cross-Sectional Studies , Sequence Analysis, DNA , Genotype
10.
Braz. j. infect. dis ; 21(4): 424-432, July-Aug. 2017. tab, graf
Article in English | LILACS | ID: biblio-888899

ABSTRACT

Abstract Hepatitis B virus (HBV) is distributed worldwide, with geographical variations regarding prevalence of the different genotypes. The aim of this study was to determine the HBV genotypes and subgenotypes circulating in Southeast Brazil and compare the genetic sequences found with HBV sequences previously described in the world. Sequences from 166 chronic HBV carriers were analyzed using the fragment constituted by 1306 base pairs comprising surface and polymerase regions of the HBV genome. The sequences obtained were submitted to phylogenetic analysis. HBV subgenotypes A1, A2, D1-D4, F2a, and F4 were found. HBV genotype D was the most frequent, found in 99 patients (58.4%). Within this group, subgenotype D3 was the most prevalent, in 73 patients (42.9%). HBV genotype A was identified in 58 (36%) patients, subgenotype A1, in 48 (29.8%) subjects. Genotype F was identified in 9 (5.4%). According to the phylogenetic analysis, the sequences found were grouped with sequences from Europe, Asia and Middle East (subgenotypes D1, D2, D3) and sequences from Latin America and Africa (subgenotype A1). HBV D3 grouped in different clusters inside D3 clade, several of them with sequences isolated in Italy. We also identified eight families whose relatives were infected with the same HBV subgenotype, most with high similarity between sequences. In conclusion, the distribution of the HBV sequences obtained interweaved with sequences from other continents, corresponding to regions from where many immigrants came to this region, in accordance to the hypothesis that the HBV detected over there were brought during the colonization times.


Subject(s)
Humans , Male , Female , Adult , Middle Aged , Aged , Young Adult , Hepatitis B virus/genetics , Hepatitis B, Chronic/virology , Emigrants and Immigrants , Phylogeny , Brazil , DNA, Viral/genetics , Molecular Sequence Data , Sequence Analysis, DNA , Emigration and Immigration , Genotype
11.
Mem. Inst. Oswaldo Cruz ; 112(7): 485-491, July 2017. tab, graf
Article in English | LILACS | ID: biblio-841815

ABSTRACT

BACKGROUND Many studies have identified mutations in the hepatitis B surface antigen (HBsAg) as important factors limiting the ability of commercial serological assays to detect this viral antigen. However, an association between mutations in the HBsAg gene and the occurrence of occult HBV infection (OBI) in patients has not been established. OBJECTIVES To detect hepatitis B virus (HBV) DNA in patients with anti-HBc as a unique serological marker, a previously published, cost-effective TaqMan-based real-time polymerase chain reaction (PCR) test with minor groove binding probes was adapted for use in this study. The current study also aimed to investigate HBsAg mutations and genotypes of HBV in OBI at the Viral Hepatitis Ambulatory Clinic in Rio de Janeiro to determine any possible association. METHODS Intra-assay and inter-assay reproducibility were determined, and the mean coefficient of variation values obtained were 2.07 and 3.5, respectively. Probit analysis indicated that the 95% detection level was 25 IU/mL. The prevalence of OBI was investigated in 35 serum samples with an ‘anti-HBc alone’ profile from individuals who attended our clinic between 2011 and 2013. FINDINGS HBV DNA was detected in only one sample, resulting in an OBI rate of 2.9%. Nucleotide sequencing of the pre-S/S region was performed to genotype and analyse mutations within the HBsAg gene of this HBV DNA. The HBV in the OBI case was classified as sub-genotype A1, and a sequence analysis of the small S gene revealed 12 mutations in the major hydrophilic region compared to the consensus A1 sequence. Most of these mutations occurred in amino acid residues that have been reported as clinically relevant because they have been implicated in vaccine escape and/or inability to detect HBsAg by commercial serological assays. MAIN CONCLUSIONS Our study suggests the importance of specific HBsAg mutations, different from those in D, B, and C genotypes, in sub-genotype A1 HBV associated with OBI.


Subject(s)
DNA, Viral/isolation & purification , DNA, Viral/genetics , Hepatitis B/genetics , Hepatitis B/virology , Hepatitis B Surface Antigens/genetics , Sensitivity and Specificity , Real-Time Polymerase Chain Reaction
12.
Mem. Inst. Oswaldo Cruz ; 112(7): 492-498, July 2017. tab
Article in English | LILACS | ID: biblio-841811

ABSTRACT

BACKGROUND Increasing evidence suggests that human papillomavirus (HPV) intratype variants (specific lineages and sublineages) are associated with pathogenesis and progression from HPV infection to persistence and the development of cervical cancer. OBJECTIVES This study aimed to verify the prevalence of HPV infection and distribution of HPV types and HPV16 variants in southern Brazil in women with normal cytology or intraepithelial lesions. METHODS HPV typing was determined by L1 gene sequencing. To identify HPV16 variants, the LCR and E6 regions were sequenced, and characteristic single nucleotide variants were identified. FINDINGS A total of 445 samples were studied, with 355 from cervical scrapes and 90 from cervical biopsies. HPV was detected in 24% and 91% of these samples, respectively. The most prevalent HPV types observed were 16 (cervical, 24%; biopsies, 57%) and 58 (cervical, 12%; biopsies, 12%). Seventy-five percent of the HPV16-positive samples were classified into lineages, with 88% defined as lineage A, 10% as lineage D, and 2% as lineage B. MAIN CONCLUSIONS This study identified a high frequency of European and North American HPV16 lineages, consistent with the genetic background of the human population in southern Brazil.


Subject(s)
Humans , Female , Adult , Genetic Variation/genetics , DNA, Viral/genetics , Uterine Cervical Neoplasms/virology , Papillomavirus Infections/virology , Human papillomavirus 16/genetics , Socioeconomic Factors , Brazil , Uterine Cervical Dysplasia , Polymerase Chain Reaction , Cross-Sectional Studies
13.
Braz. j. infect. dis ; 21(3): 297-305, May-June 2017. tab
Article in English | LILACS | ID: biblio-839207

ABSTRACT

ABSTRACT The present study evaluated several techniques currently available (commercial kits and in-house assays) for diagnosing human T lymphotropic viruses types 1 and 2 in two groups of patients enrolled at HIV/AIDS specialized care services in São Paulo: Group 1 (G1), n = 1608, 1237 male/371 female, median age 44.3 years old, majority using highly active antiretroviral therapy (HAART); G2, n = 1383, 930 male/453 female, median age of 35.6 years old, majority HAART naïve. Enzyme immunoassays [(EIA) Murex and Gold ELISA] were employed for human T lymphotropic viruses types 1 and 2 screening; Western blotting (WB), INNO-LIA (LIA), real-time PCR pol (qPCR), and nested-PCR-RFLP (tax) were used to confirm infection. Samples were considered human T lymphotropic viruses types 1 and 2 positive when there was reactivity using at least one of the four confirmatory assays. By serological screening, 127/2991 samples were positive or borderline, and human T lymphotropic virus infection was confirmed in 108 samples (three EIA-borderline): 56 human T lymphotropic virus type 1 [G1 (27) + G2 (29)]; 45 human T lymphotropic virus type 2 [G1 (21) + G2 (24)]; one human T lymphotropic virus type 1 + human T lymphotropic virus type 2 (G2); six human T lymphotropic virus [G1 (2) + G2 (4)]. Although there were differences in group characteristics, human T lymphotropic viruses types 1 and 2 prevalence was similar [3.1% (G1) and 4.2% (G2), p = 0.113]. The overall sensitivities of LIA, WB, qPCR, and PCR-RFLP were 97.2%, 82.4%, 68.9%, and 68.4%, respectively, with some differences among groups, likely due to the stage of human T lymphotropic virus infection and/or HAART duration. Indeterminate immunoblotting results were detected in G2, possibly due to the seroconversion period. Negative results in molecular assays could be explained by the use of HAART, the occurrence of defective provirus and/or the low circulating proviral load. In conclusion, when determining the human T lymphotropic virus infection, the findings highlight that there is a need to consider the blood samples with borderline results in screening assays. Of all the tested assays, LIA was the assay of choice for detecting human T lymphotropic virus type 1 and human T lymphotropic virus type 2 in human immunodeficiency virus type 1-infected patients.


Subject(s)
Humans , Male , Female , Adult , HTLV-I Infections/diagnosis , HTLV-II Infections/diagnosis , HIV Infections/complications , DNA, Viral/genetics , Enzyme-Linked Immunosorbent Assay , HTLV-I Antibodies/blood , HTLV-I Infections/complications , HTLV-II Antibodies/blood , HTLV-II Infections/complications , Blotting, Western , Sensitivity and Specificity , Real-Time Polymerase Chain Reaction
14.
Mem. Inst. Oswaldo Cruz ; 112(3): 220-223, Mar. 2017. tab, graf
Article in English | LILACS | ID: biblio-841773

ABSTRACT

The use of quantitative real time polymerase chain reaction (qPCR) for herpesvirus detection has improved the sensitivity and specificity of diagnosis, as it is able to detect shedding episodes in the absence of clinical lesions and diagnose clinical specimens that have low viral loads. With an aim to improve the detection and quantification of herpesvirus by qPCR, synthetic standard curves for human herpesvirus 1 and 2 (HHV-1 and HHV-2) targeting regions gD and gG, respectively, were designed and evaluated. The results show that synthetic curves can replace DNA standard curves in diagnostic herpes qPCR.


Subject(s)
Humans , Herpesvirus 2, Human/genetics , Herpesvirus 1, Human/genetics , Herpes Simplex/virology , DNA, Viral/genetics , Sensitivity and Specificity , Viral Load , Real-Time Polymerase Chain Reaction , Herpes Simplex/diagnosis
15.
Mem. Inst. Oswaldo Cruz ; 112(3): 175-181, Mar. 2017. tab, graf
Article in English | LILACS | ID: biblio-841776

ABSTRACT

BACKGROUND Two novel viruses named circo-like virus-Brazil (CLV-BR) hs1 and hs2 were previously discovered in a Brazilian human fecal sample through metagenomics. CLV-BR hs1 and hs2 possess a small circular DNA genome encoding a replication initiator protein (Rep), and the two genomes exhibit 92% nucleotide identity with each other. Phylogenetic analysis based on the Rep protein showed that CLV-BRs do not cluster with circoviruses, nanoviruses, geminiviruses or cycloviruses. OBJECTIVE The aim of this study was to search for CLV-BR genomes in sewage and reclaimed water samples from the metropolitan area of São Paulo, Brazil, to verify whether the first detection of these viruses was an isolated finding. METHODS Sewage and reclaimed water samples collected concomitantly during the years 2005-2006 were purified and concentrated using methodologies designed for the study of viruses. A total of 177 treated reclaimed water samples were grouped into five pools, as were 177 treated raw sewage samples. Nucleic acid extraction, polymerase chain reaction (PCR) amplification and Sanger sequencing were then performed.e FINDINGS CLV-BR genomes were detected in two pools of sewage samples, p6 and p9. Approximately 28% and 51% of the CLV-BR genome was amplified from p6 and p9, respectively, including 76% of the Rep gene. The detected genomes are most likely related to CLV-BR hs1. Comparative analysis showed several synonymous substitutions within Rep-encoding sequences, suggesting purifying selection for this gene, as has been observed for other eukaryotic circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses. MAIN CONCLUSION The results therefore indicated that CLV-BR has continued to circulate in Brazil two and three years after first being detected.


Subject(s)
Humans , Sewage/virology , DNA, Viral/genetics , Polymerase Chain Reaction , Circovirus/isolation & purification , Circovirus/genetics , Phylogeny , Genome, Viral , Sequence Analysis
16.
Braz. j. otorhinolaryngol. (Impr.) ; 83(1): 38-44, Jan.-Feb. 2017. tab
Article in English | LILACS | ID: biblio-839410

ABSTRACT

Abstract Introduction Molecular studies about carcinomas of the oral cavity and oropharynx demonstrate the presence of human papilomavirus genome in these tumors, reinforcing the participation of human papilomavirus in oral carcinogenesis. Objectives This study aimed to determine the prevalence of human papilomavirus and genotype distribution of HPV16 and HPV18 in oral cavity and oropharynx carcinomas, as well as their association with clinical characteristics of the tumors. Methods This is a retrospective study, with clinical data collected from 82 patients. Human papilomavirus detection was conducted on specimens of oral cavity and oropharynx carcinomas included in paraffin blocks. Patients were assisted in a cancer reference center, in the central region of Brazil, between 2005 and 2007. Polymerase chain reaction was used for the detection and genotyping of human papilomavirus. Results Among the patients evaluated, 78% were male. The average age of the group was about 58 years. Risk factors, such as smoking (78%) and alcohol consumption (70.8%) were recorded for the group. HPV DNA was detected in 21 cases (25.6%; 95% confidence interval 16.9–36.6) of which 33.3% were HPV16 and 14.3% were HPV18. The presence of lymph node metastases and registered deaths were less frequent in human papilomavirus positive tumors, suggesting a better prognosis for these cases; however, the differences between the groups were not statistically significant. Conclusion The results obtained in the present study, with respect to the presence of the high-risk HPV16 and HPV18 genotypes, highlight the importance of human papilomavirus vaccination in the control of oral cavity and oropharynx carcinomas.


Resumo Introdução Estudos moleculares sobre carcinomas da cavidade oral e orofaringe demonstram a presença do genoma do papilomavírus humano (HPV) nesses tumores, o que enfatiza a participação do HPV na carcinogênese oral. Objetivos Determinar a prevalência de HPV e a distribuição genotípica de HPV16 e HPV18 nos carcinomas de cavidade oral e orofaringe, bem como sua associação com as características clínicas dos tumores. Método Estudo retrospectivo, com dados clínicos coletados de 82 pacientes. A detecção de HPV foi feita em amostras de carcinomas de cavidade oral e orofaringe incluídos em blocos de parafina. Os pacientes foram atendidos em um centro de referência para tratamento do câncer, na região central do Brasil, entre 2005 e 2007. Foi usada a reação em cadeia de polimerase (PCR) para a detecção e genotipagem do HPV. Resultados Entre os pacientes avaliados, 78% eram homens. A média de idade do grupo era de 58 anos. Fatores de risco como o tabagismo (78%) e consumo de álcool (70,8%) foram registrados para o grupo. HPV DNA foi detectado em 21 casos (25,6%; IC de 95%, 16,9-36,6), dos quais 33,3% eram HPV16 e 14,3% eram HPV18. A presença de metástases em linfonodos e os óbitos registrados foram menos frequentes em tumores positivos para HPV, o que sugere melhor prognóstico para esses casos; contudo, as diferenças entre os grupos não foram estatisticamente significantes. Conclusão Os resultados obtidos no presente estudo, com respeito à presença de genótipos de alto risco de HPV16 e HPV18, destacam a importância da vacinação para HPV no controle dos carcinomas de cavidade oral e orofaringe.


Subject(s)
Humans , Male , Female , Middle Aged , Oropharyngeal Neoplasms/virology , Papillomavirus Infections/genetics , Papillomavirus Infections/virology , Human papillomavirus 16/genetics , Human papillomavirus 18/genetics , Mouth/virology , Brazil , DNA, Viral/genetics , Polymerase Chain Reaction , Retrospective Studies , Risk Factors , Human papillomavirus 18/isolation & purification , Genotype
17.
Braz. j. microbiol ; 47(2): 513-517, Apr.-June 2016. tab, graf
Article in English | LILACS | ID: lil-780838

ABSTRACT

Abstract Ungulate tetraparvovirus 2 (UTV2) , formerly known as porcine hokovirus due to its discovery in Hong Kong, is closely related to a Primate tetraparvovirus (human PARV-4) and Ungulate tetraparvovirus 1 (bovine hokovirus). Until now, UTV2 was detected in European, Asian and North American countries, but its occurrence in Latin America is still unknown. This study describes the first report of UTV2 in Brazil, as well as its phylogenetic characterization. Tissue samples (lymph node, lung, liver, spleen and kidney) of 240 piglets from eight different herds (30 animals each herd) were processed for DNA extraction. UTV2 DNA was detected by PCR and the entire VP1/VP2 gene was sequenced for phylogenetic analysis. All pigs from this study displayed postweaning multisystemic wasting syndrome (PMWS). UTV2 was detected in 55.3% of the samples distributed in the variety of porcine tissues investigated, as well as detected in almost all herds, with one exception. The phylogenetic analysis demonstrated that Brazilian UTV2 sequences were more closely related to sequences from Europe and United States.


Subject(s)
Animals , Phylogeny , Swine Diseases/virology , Parvoviridae Infections/veterinary , Parvovirinae/isolation & purification , Parvovirinae/classification , Swine , Brazil , DNA, Viral/genetics , Parvoviridae Infections/virology , Parvovirinae/genetics
18.
Braz. j. infect. dis ; 20(2): 173-178, Mar.-Apr. 2016. tab
Article in English | LILACS | ID: lil-780801

ABSTRACT

Abstract Objective There are a lot of disagreements in the studies on hepatitis B virus (HBV) DNA polymerase mutation rate associated with nucleos(t)ide analogues (NAs) in treatment-naive chronic hepatitis B (CHB) patients. This is the first study aimed to investigate the prevalence of spontaneous HBV resistance mutations in Central China. Methods This study included treatment-naive patients with CHB from June 2012 to May 2015 receiving care at the Institute of Liver Disease in Central China. All patients completed a questionnaire covering different aspects, such as family medical history, course of liver disease, medication history, alcohol use, among others. Mutations in HBV DNA polymerase associated with NAs resistance were detected using INNO-LiPA assay. Results 269 patients were infected with HBV genotype B (81.4%), C (17.9%), and both B and C (0.7%). Mutations in HBV DNA polymerase were detected in 24 patients (8.9%) including rtM204I/V (n = 6), rtN236T (n = 5), rtM250V (n = 2), rtL180M (n = 2), rtT184G (n = 1), rtM207I (n = 1), rtS202I (n = 1), rtM204V/I & rtL180M (n = 5), and rtM204I & rtM250V (n = 1). Conclusion Spontaneous HBV resistance mutations in HBV DNA polymerase were found in treatment-naive patients with CHB in Central China. These findings suggest that we should analyze HBV DNA polymerase resistance mutation associated with NAs before giving antiviral therapy such as lamivudine (LAM), adefovir (ADV), and telbivudine (LdT).


Subject(s)
Humans , Male , Female , Pregnancy , Adult , Middle Aged , Aged , Young Adult , DNA, Viral/genetics , Hepatitis B virus/genetics , Hepatitis B, Chronic/virology , Drug Resistance, Viral/genetics , DNA-Directed DNA Polymerase/genetics , Mutation/genetics , Antiviral Agents/therapeutic use , China , Hepatitis B virus/drug effects , Prevalence , Prospective Studies , Hepatitis B, Chronic/drug therapy , Genotype
19.
Braz. j. microbiol ; 47(1): 243-250, Jan.-Mar. 2016. tab, graf
Article in English | LILACS | ID: lil-775111

ABSTRACT

Abstract Human adenovirus species F (HAdV-F) type 40 and 41 are commonly associated with acute diarrheal disease (ADD) across the world. Despite being the largest state in southeastern Brazil and having the second largest number of inhabitants, there is no information in the State of Minas Gerais regarding the role of HAdV-F in the etiology of ADD. This study was performed to determine the prevalence, to verify the epidemiological aspects of infection, and to characterize the strains of human adenoviruses (HAdV) detected. A total of 377 diarrheal fecal samples were obtained between January 2007 and August 2011 from inpatient and outpatient children of age ranging from 0 to 12 years. All samples were previously tested for rotavirus, norovirus, and astrovirus, and 314 of 377 were negative. The viral DNA was extracted, amplified using the polymerase chain reaction and the HAdV-positive samples were sequenced and phylogenetically analyzed. Statistical analyses were performed using the Chi-square test (p < 0.05), considering two conditions: the total of samples tested (377) and the total of negative samples for the remaining viruses tested (314). The overall prevalence of HAdV was 12.47% (47/377); and in 76.60% (36/47) of the positive samples, this virus was the only infectious agent detected. The phylogenetic analysis of partial sequences of 32 positive samples revealed that they all clustered with the HAdV-F type 41. The statistical analysis showed that there was no correlation between the onset of the HAdV infection and the origin of the samples (inpatients or outpatients) in the two conditions tested: the total of samples tested (p = 0.598) and the total of negative samples for the remaining viruses tested (p = 0.614). There was a significant association in the occurrence of infection in children aged 0–12 months for the condition 1 (p = 0.030) as well as condition 2 (p = 0.019). The occurrence of infections due to HAdV did not coincide with a pattern of seasonal distribution. These data indicate the significant involvement of HAdV-F type 41 in the etiology of ADD in Minas Gerais, which demonstrates the importance of other viral agents in the development of the disease after the introduction of rotavirus vaccine immunization.


Subject(s)
Child , Child, Preschool , Humans , Infant , Infant, Newborn , Adenovirus Vaccines/administration & dosage , Adenoviruses, Human/isolation & purification , Diarrhea/epidemiology , Diarrhea/prevention & control , Rotavirus Infections/epidemiology , Rotavirus Infections/prevention & control , Adenovirus Vaccines/immunology , Adenoviruses, Human/classification , Adenoviruses, Human/genetics , Brazil/epidemiology , Cluster Analysis , DNA, Viral/chemistry , DNA, Viral/genetics , DNA, Viral/isolation & purification , Feces/virology , Genotype , Phylogeny , Prevalence , Sequence Analysis, DNA
20.
Braz. j. microbiol ; 47(1): 217-224, Jan.-Mar. 2016. tab, graf
Article in English | LILACS | ID: lil-775123

ABSTRACT

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.


Subject(s)
Animals , Bird Diseases/virology , Genotype , Herpesviridae Infections/veterinary , Herpesviridae/classification , Herpesviridae/isolation & purification , Brazil , DNA, Viral/genetics , Herpesviridae Infections/virology , Herpesviridae/genetics , Parrots , Polymerase Chain Reaction , Polymorphism, Restriction Fragment Length
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