ABSTRACT
Introducción: La infección persistente por genotipos de virus papiloma humano de alto riesgo (VPH-AR) es la principal causa del cáncer cérvico-uterino en todo el mundo. Los genotipos 16 y 18 están asociados a la progresión hacia el cáncer de cuello uterino; sin embargo, otros genotipos también presentan alto riesgo oncogénico. Existe escasa evidencia respecto a la distribución de genotipos VPH-AR en la población nacional, siendo un tema que debiese ser abordado en el contexto de un creciente aumento de la inmigración e implementación del programa de inmunización en Chile desde 2015. Objetivo: Dar a conocer la distribución de genotipos de VPH-AR detectados en pacientes de ambos sexos, atendidos en la red de atención privada de Clínica Dávila de Santiago, entre los años 2014 y 2021. Metodología: Se estudiaron muestras genitales y anales provenientes de 3.642 pacientes, incluyendo ambos sexos. La genotipificación fue realizada mediante reacción de la polimerasa en cadena (RPC) en tiempo real (HPV AnyplexTM II HPV28 detection, Seegene, Korea. Resultados: La distribución global de genotipos en mujeres (porcentaje) fue: 16 (14,34%) - 31 (6,20%) - 39 (5,94%) - 58 (5,94%) - 51 (5,68%) - 53 (5,64%) - 52 (5,30%) - 56 (5,27%) - 68 (5,19%) - 66 (4,97% - 18 (3,36%) - 59 (3,29%) - 73 (2,80%) - 35 (2,54%) - 45 (2,13%) - 33 (1,53%) - 82 (1,38%) - 26 (0,49%) y 69 (0,41%). En hombres fue: 16 (8,52%) - 58 (4,39%) - 51 (8,44%) - 26 (0,42%) - 18 (3,21%) - 52 (4,47%) - 39 (5,40%) - 53 (4,56%) - 33 (1,69%) - 35 (2,03%), 73 (2,19%) - 69 (0,59%) - 45 (2,11%) - 59 (4,22%) - 68 (3,04%) - 66 (5,06%) - 31 (4,64%) - 56 (4,81%) y 82 (1,10%). Conclusiones: La distribución de los genotipos de VPH fue concordante con estudios previos nacionales. Se observó una tendencia a la reducción del genotipo 16 en el tiempo, lo cual podría relacionarse a la vacunación, implementada en los últimos años en Chile. Destaca que otros genotipos de VPH-AR tuvieron una alta frecuencia en la población estudiada por lo que sería recomendable evaluar la pesquisa ampliada de genotipos de VPH-AR para valorar el riesgo oncogénico, con fines diagnósticos y terapéuticos.
Background: Persistent infection by high-risk human papillomavirus (HR-HPV) genotypes is the main cause of cervical cancer worldwide. Genotypes 16 and 18 are associated with progression to cervical cancer, however other genotypes also present high oncogenic risk. There is little evidence regarding the distribution of HR-HPV genotypes in the national population, being an issue that should be addressed in the context of a growing increase in immigration and implementation of the immunization program in Chile since 2015. Aim: To show the distribution of HR-HPV genotypes detected in women and men, attended at the private care network of Clinica Davila, Santiago City, between 2014 and 2021. Methods: Genital and anal samples from 3,642 patients were studied, including both sexes. Genotyping was performed by real-time polymerase chain reaction (PCR) (HPV AnyplexTM II HPV28 detection, Seegene, Korea). Results: The global distribution of genotypes in women (percentage) was: 16 (14.34%) - 31 (6.20%) - 39 (5.94%) - 58 (5.94%) - 51 (5.68%) - 53 (5.64%) - 52 (5.30%) - 56 (5.27%) - 68 (5.19%) - 66 (4.97%) - 18 (3.36%) - 59 (3.29%) - 73 (2.80%) - 35 (2.54%) - 45 (2.13%) - 33 (1.53%) - 82 (1.38%) - 26 (0.49%) and 69 (0.41%). In men was: 16 (8.52%) - 58 (4.39%) - 51 (8.44%) - 26 (0.42%) - 18 (3.21%) - 52 (4.47%) - 39 (5.40%) - 53 (4.56%), 33 (1.69%) - 35 (2.03%) - 73 (2.19%) - 69 (0.59%) - 45 (2.11%) - 59 (4.22%) - 68 (3.04%) - 66 (5.06%) - 31 (4.64%) - 56 (4.81%) and 82 (1.10%). Conclusions: The distribution of HPV genotypes was consistent with previous national studies. A tendency to reduce genotype 16 over the years was observed, which could be related to the vaccination, implemented in recent years in Chile. It is remarkable that other HR-HPV genotypes had a high frequency in the population studied, so it would be advisable to evaluate an expanded screening for HR-HPV genotypes to assess the oncogenic risk, for diagnostic and therapeutic purposes.
Subject(s)
Humans , Male , Female , Papillomavirus Infections/epidemiology , Papillomaviridae/genetics , DNA, Viral/genetics , Chile/epidemiology , Prevalence , Cross-Sectional Studies , Risk Assessment , Papillomavirus Infections/virology , Human papillomavirus 16/genetics , Human papillomavirus 18/genetics , Genotyping Techniques , Real-Time Polymerase Chain Reaction , Genotype , Papillomaviridae/isolation & purification , Health Facilities, ProprietaryABSTRACT
INTRODUCCIÓN: El virus del papiloma humano de alto riesgo (VPH-AR) es responsable del cáncer de cuello uterino y sus lesiones preneoplásicas. Los genotipos VPH16 y VPH18 son los más frecuentes en este cáncer. La integración del VPH-AR en el genoma de la célula hospedera es crucial en la carcinogénesis cervical, pero la etapa en que ocurre en la población chilena es incierta. OBJETIVO: Evaluar la integración de VPH16 y VPH18 en lesiones pre-neoplásicas de cuello uterino. MÉTODOS: Se analizaron 108 muestras de raspados cervicales. El VPH se genotipificó mediante reacción de polimerasa en cadena (RPC) e hibridación no radiactiva. La integración de VPH16 y VPH18 se determinó por presencia del gen E2 mediante RPC. RESULTADOS: VPH16 y VPH18 se detectaron en 36,1% y 12,0% de las muestras, respectivamente. El VPH16 se integró en 23,1% de los casos de VPH16, mientras que VPH18 se integró en 100% de las muestras positivas para este genotipo. CONCLUSIONES: La integración VPH-AR es un evento temprano en la carcinogénesis cervical que ocurre en casi la mitad de las lesiones pre-neoplásicas y es más frecuente en VPH18 que en VPH16. La evaluación de la integración VPH-AR puede ser una herramienta útil para detectar el virus en la población chilena.
BACKGROUND: High-risk Human Papillomaviruses (HR-HPVs) are the etiological agents of cervical cancer and its preneoplastic lesions. HPV16 and 18 are the most frequent HR-HPV genotypes detected in cervical cancer. HR-HPV genome integration into the host cell is an important event in the carcinogenic process. However, it remains uncertain which stage of cervical carcinogenesis HPV16 and 18 integration occurs in the Chilean population. AIM: The goal of this study was to evaluate HPV16 and HPV18 integration in preneoplastic lesions of the cervix. METHODS: DNA was extracted from 108 cervical scrape samples with preneoplastic lesions. HPV was genotyped using PCR and non-radioactive hybridization. The integration status of HPV16 and HPV 18 was determined by evaluating the E2 gene presence through PCR. RESULTS: HPV16 and HPV18 tested positive in 36.1% and 12.0% of samples, respectively. HPV16 was found integrated in 23.1% of HPV 16 cases, while HPV 18 in 100% of samples positive for this viral genotype. CONCLUSIONS: HR-HPV integration is an early event in cervical carcinogenesis, occurring in nearly half of preneoplastic lesions and being more frequent in HPV18 than in HPV16. The evaluation of HR-HPV integration can be utilized as a complementary tool for detecting HPV in the Chilean population.
Subject(s)
Humans , Female , Adolescent , Adult , Middle Aged , Young Adult , Precancerous Conditions/virology , Cervix Uteri/virology , Virus Integration/genetics , Papillomaviridae/isolation & purification , Papillomaviridae/genetics , Precancerous Conditions/genetics , DNA, Viral/genetics , Cervix Uteri/pathology , Chile , Polymerase Chain Reaction , Cross-Sectional Studies , Human papillomavirus 16/isolation & purification , Human papillomavirus 16/genetics , Human papillomavirus 18/isolation & purification , Human papillomavirus 18/genetics , Genotyping Techniques , GenotypeABSTRACT
The resolution of the hepatitis C issue has raised expectations for a chronic hepatitis B cure, driving the industry to expand investment in research and development efforts to strengthen functional cure strategies. These strategies have a wide variety of types, and the published research findings are heterogeneous. The theoretical analysis of these strategies is of great significance for determining prioritized research orientations as well as sensibly allocating research and development resources. However, due to a paucity of necessary conceptual models, current theoretical analysis has not been able to unify various therapeutic strategies into a proper theoretical framework. In view of the fact that the decrease in the quantity of cccDNA is an inevitable core event accompanied by the process of functional cure, this paper intends to analyze several chronic hepatitis B cure strategies using cccDNA dynamics as a framework. Furthermore, there are currently few studies on the dynamics of the cccDNA field, hoping that this article can promote recognition and research in this field.
Subject(s)
Humans , Hepatitis B virus/genetics , Hepatitis B, Chronic/drug therapy , Antiviral Agents/therapeutic use , Virus Replication , DNA, Circular/therapeutic use , DNA, Viral/genetics , Hepatitis B/drug therapyABSTRACT
INTRODUCCIÓN: En Chile, el cáncer de cuello uterino (CCU) es la segunda causa de muerte por neoplasias malignas en la mujer. El principal agente causal es el virus papiloma humano (VPH). Comparando con la población general, los o las trabajadoras(es) sexuales (TS) tienen alto riesgo de adquirir VPH. OBJETIVO: Analizar la prevalencia y genotipos del VPH cervical y vaginal en TS que se atienden en un Centro de Salud Sexual de Santiago, Chile. Pacientes y MÉTODO: Se realizó un estudio transversal en 97 mujeres TS, de 19 a 70 años de edad. Se obtuvieron dos muestras por paciente, una de exocérvix y otra de paredes vaginales. El ADN de VPH fue identificado por reacción de polimerasa en cadena (RPC) y su genotipo fue investigado para 32 tipos de VPH. RESULTADOS: La prevalencia de VPH global fue de 45%, observándose portación cervical en 41,2% y vaginal en 36,1%, con una coinfección de 32%. El 63% de las muestras tenía genotipos de alto riesgo. Los VPH de alto riesgo más frecuentes fueron el VPH 66 (12%), VPH 58 (9,3%), seguidos por VPH 16, VPH 59 y VPH 82 con igual frecuencia (8% c/u). Treinta y dos mujeres (43%) fueron infectadas con genotipos múltiples. CONCLUSIÓN: El VPH es una infección frecuente entre las TS. Este es el primer estudio en Chile sobre prevalencia y genotipos de VPH en TS.
BACKGROUND: In Chile, cervical cancer is the second leading cause of death from malignancy in women. The main causal agent of cervical cancer is the human papillomavirus (HPV). Compared with the general population, sex workers (SW) are at increased risk of acquiring HPV. AIM: To analyze the prevalence and genotypes of cervical and vaginal HPV in female SW attending a Sexual Control Centre. METHODS: A cross-sectional study was carried out on 97 women (19-70 years old). Two samples were taken per patient, one from exocervix and the other from vaginal walls. HPV DNA. was identified by polymerase chain reaction (PCR) and genotyping using specific probes for 32 types of HPV. RESULTS: The overall frequency of HPV was 45%, 41.2% in cervical carrier and 36.1% in vaginal carrier, 32% were co-infected, 63% of HPV were high-risk genotypes. The most frequent high-risk HPV was HPV 66 (12%), HPV 58 (9.3%), followed by HPV 16, HPV 59 and HPV 82 with the same frequency (8% each one). Thirty two (43%) of females were infected with multiple genotypes. CONCLUSION: HPV is frequent infection among SW. This is the first study in Chile on the prevalence and genotypes of HPV in sex workers.
Subject(s)
Humans , Female , Adult , Middle Aged , Aged , Young Adult , Uterine Cervical Neoplasms/pathology , Uterine Cervical Neoplasms/epidemiology , Papillomavirus Infections/epidemiology , Alphapapillomavirus/genetics , Sex Workers , Papillomaviridae/genetics , DNA, Viral/analysis , DNA, Viral/genetics , Chile/epidemiology , Prevalence , Cross-Sectional Studies , GenotypeABSTRACT
Objective: To investigate the influencing factors of HBV intrauterine transmission and their interaction effects by integrating logistic regression model and Chi-squared automatic interaction detector (CHAID) decision tree model. Methods: A total of 689 pairs of HBsAg-positive mothers and their neonates in the obstetrics department of the Third People's Hospital of Taiyuan from 2007 to 2013 were enrolled, and the basic information of mothers and their neonates were obtained by questionnaire survey and medical record review, such as the general demographic characteristics, gestational week and delivery mode. HBV DNA and HBV serological markers of the mothers and newborns were detected by fluorescence quantitative PCR and electrochemiluminescence immunoassay respectively. The CHAID decision tree model and unconditional logistic regression analysis were used to explore the factors influencing HBV intrauterine transmission in neonates of HBsAg-positive mothers. Results: Among the 689 neonates, the incidence of HBV intrauterine transmission was 11.47% (79/689). After adjusted for confounding factors, the first and second logistic multivariate analysis showed that cesarean delivery was a protective factor for HBV intrauterine transmission (OR=0.25, 95%CI: 0.14-0.43; OR=0.27, 95%CI: 0.15-0.46); both models indicated that maternal HBeAg positivity and HBV DNA load ≥2×105 IU/ml before delivery were risk factors of HBV intrauterine transmission (OR=3.89, 95%CI: 2.32-6.51; OR=3.48, 95%CI: 2.12-5.71), respectively. The CHAID decision tree model screened three significant factors influencing HBV intrauterine transmission, the most significant one was maternal HBeAg status, followed by delivery mode and maternal HBV DNA load. There were interactions between maternal HBeAg status and delivery modes, as well as delivery mode and maternal HBV DNA load before delivery. The rate of HBV intrauterine transmission in newborns of HBeAg-positive mothers by vaginal delivery increased from 19.08% to 29.37%; among HBeAg-positive mothers with HBV DNA ≥2×105 IU/ml, the rate of HBV intrauterine transmission increased to 33.33% in the newborns by vaginal delivery. Conclusions: Maternal HBeAg positivity,maternal HBV DNA ≥2×105 IU/ml and vaginal delivery could be risk factors for HBV intrauterine transmission in newborns. Interaction effects were found between maternal HBeAg positivity and vaginal delivery, as well as vaginal delivery and high maternal HBV DNA load. Logistic regression model and the CHAID decision tree model can be used in conjunction to identify the high-risk populations and develop preventive strategies accurately.
Subject(s)
Female , Humans , Infant, Newborn , Pregnancy , DNA, Viral/genetics , Decision Trees , Hepatitis B Surface Antigens , Hepatitis B e Antigens , Hepatitis B virus/genetics , Infectious Disease Transmission, Vertical , Logistic Models , Mothers , Pregnancy Complications, Infectious/epidemiologyABSTRACT
Objective: To investigate the type, length, and CG loci of HBV DNA CpG islands in HBsAg positive maternal C genotype and its relationship with intrauterine HBV transmission, so as to provide a new perspective for the study of intrauterine transmission of HBV. Methods: From June 2011 to July 2013, HBsAg-positive mothers and their newborns who delivered in the obstetrics and gynecology department of the Third People's Hospital of Taiyuan were collected. Epidemiological data were collected through face-to-face questionnaires and electronic medical records. Serum HBV markers and serum HBV DNA were detected by electrochemiluminescence and quantitative fluorescence PCR, respectively. Intrauterine transmission of HBV was determined by positive HBsAg and/or HBV DNA in femoral venous blood before injection of HBV vaccine/Hepatitis B immunoglobulin within 24 h of birth. A total of 22 mothers and their newborns with HBV DNA load ≥106 IU/ml in intrauterine transmission were selected as the intrauterine transmission group, and 22 mothers with HBV DNA load ≥106 IU/ml without intrauterine transmission were chosen as the control group by random seed method. The distribution prediction of CpG islands of HBV DNA in 39 mothers with genotype C by HBV DNA sequencing was analyzed. Results: Among 39 mothers with HBV C genotype, 19 were in the intrauterine transmission group, and 20 were in the control group. The HBV DNA of 39 patients with genotype C traditional CpG island Ⅱ and Ⅲ, while the control group had traditional CpG island Ⅰ and novel CpG island Ⅳ and Ⅴ. The length of CpG island Ⅱ and Ⅲ and the number of CG loci of CpG island Ⅱ in the intrauterine transmission group differed from those in the control group (P<0.05). The CpG island Ⅱ length ≥518 bp and the number of CG loci ≥40 in the intrauterine transmission group (11/19) were significantly higher than those in the control group (2/20) (P<0.05). The length of CpG island Ⅱ and the number of CG loci in the X gene promoter region (Xp region) were higher than those in the control group (P<0.05). In the HBV intrauterine transmission group, most of maternal (12/19) HBV DNA CpG island Ⅱ completely covered the Xp region, which was significantly higher than that in the control group (5/20), and the number of HBV DNA Xp region CG loci was higher than that in the control group (P<0.05). Conclusions: The distribution of maternal C genotype HBV DNA CpG islands is related to intrauterine transmission. The length of CpG island Ⅱ and the number of CG sites may increase the risk of intrauterine transmission of HBV.
Subject(s)
Female , Humans , Infant, Newborn , Pregnancy , Biomarkers , CpG Islands , DNA, Viral/genetics , Hepatitis B , Hepatitis B Surface Antigens , Hepatitis B virus/genetics , Infectious Disease Transmission, Vertical , Mothers , Pregnancy Complications, InfectiousABSTRACT
Resumen En un estudio epidemiológico realizado previamente en Argentina, se analizó la secuencia de un fragmento del gen US5 del virus de la laringotraqueítis infecciosa (ILTV), lo que permitió diferenciar las cepas de campo de las vacunales. También esto permitió definir cinco haplotipos del ILTV, con variaciones específicas en las posiciones 461, 484, 832, 878 y 894 del gen US5. La caracterización de las cepas virales también puede lograrse mediante el análisis de la disociación de alta resolución o high-resolution melting analysis (HRMA), descripto como un método efectivo, rápido y sensible para detectar mutaciones en productos de PCR. En el presente estudio se desarrolló un protocolo de disociación de alta resolución con el objetivo de caracterizar cepas del ILTV circulantes en Argentina. Para ello,se confirmó la especificidad de esta herramienta en diferentes diluyentes del ADN de las muestras, sin observarse interferencias en presencia de ADN heterólogo u otros metabolitos celulares. Asimismo, la concentración de sales en el buffer de elución utilizado durante la extracción de ADN no alteró los perfiles de las curvas. Se obtuvieron perfiles bien definidos con concentraciones de ADN más elevadas (Ct = 26.0), mientras que concentraciones más bajas presentaron curvas heterogéneas (Ct = 32.5). El HRMA mostró una concordancia del 97.49% con la técnica de referencia, la secuenciación. El protocolo de disociación de alta resolución amplifica el ADN antes de su caracterización, por lo que esta técnica podría ser eventualmente utilizada para confirmar la presencia del ILTV y, al mismo tiempo, distinguir haplotipos, optimizando su valor como herramienta de diagnóstico. Esta característica implica una reducción significativa en el tiempo dedicado al procesamiento de muestras.
Subject(s)
Polymerase Chain Reaction , Herpesvirus 1, Gallid , DNA, Viral/genetics , Herpesvirus 1, Gallid/geneticsABSTRACT
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/epidemiologyABSTRACT
Abstract INTRODUCTION: Hepatitis B virus (HBV) infection is a public health problem; therefore, we aimed to report HBV genotypes in Ceará, Brazil. METHODS: A total of 103 HBsAg-positive samples were subjected to HBV genotyping and subgenotyping. RESULTS: The following genetic compositions of samples were found: F-54% (F2-83.33%), A-40% (A1-65%), D-6%, C2-1%, E-1%, and G-1%. CONCLUSIONS: Some genotypes are only prevalent in certain parts of the world; however, the State of Ceará is a hub for migration and has one of the most important liver transplantation centers in Brazil, which can explain the prevalence of the F genotype.
Subject(s)
Humans , Gastroenterology , Hepatitis B/epidemiology , Brazil/epidemiology , DNA, Viral/genetics , Hepatitis B virus/genetics , Prevalence , Genotype , Hepatitis B Surface AntigensABSTRACT
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 SystemABSTRACT
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)
Humans , COVID-19 , Coronavirus Infections/virology , DNA, Viral/genetics , Eye Diseases/virology , Pandemics , Pneumonia, Viral/virology , Research/trends , Virus Diseases/virologyABSTRACT
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 , Humans , Male , Young Adult , Condylomata Acuminata/virology , DNA, Viral/genetics , Genotype , Papillomaviridae/genetics , Papillomavirus Infections/virologyABSTRACT
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/geneticsABSTRACT
OBJECTIVE@#This study aimed to investigate DNA sequences that are substantially homologous to the corresponding RNA sequence sections of the hepatitis C virus (HCV). These DNA sequences are present in the whole DNA extracted from peripheral blood mononuclear cells (PBMCs) of HCV-negative subjects. We presumed that these experimentally proven 5'-noncoding region (5'-NCR) homologous DNA sequences could be contained in the extrachromosomal circular DNA (eccDNA) fraction as part of the whole cellular DNA.@*METHODS@#Home-made polymerase chain reaction (PCR) with whole cellular and isolated eccDNA, nucleotide basic local alignment search tool (BLASTn) alignments, and tests for patterns of methylation in selected sequence sections were performed.@*RESULTS@#The PCR tests revealed DNA sequences of up to 320 bp that broadly matched the corresponding sequence sections of known HCV genotypes. In contrast, BLASTn alignment searches of published HCV 5'-NCR sequences with human genome databases revealed only sequence segments of up to 36 bp of the 5'-NCR. The composition of these sequences shows missing base pairs, base pair mismatches as well as complete homology with HCV reference sequences. These short sequence sections are present in numerous copies on both the same and different chromosomes. The selected sequence region within the DNA sequences of the 5'-NCR revealed a broad diversity of individual patterns of methylation.@*CONCLUSIONS@#The experimental results confirm our assumption that parts of the HCV 5'-NCR genomic RNA sequences are present at the DNA level in the eccDNA fraction of PBMCs. The tests for methylation patterns therein revealed individual methylomes which could represent an epigenetic feature. The respective sequence section might be subject to genetic regulation.
Subject(s)
Humans , Computational Biology , DNA Methylation , DNA, Circular/genetics , DNA, Viral/genetics , Genome, Human , Genomics , Genotype , Hepacivirus/genetics , Hepatitis C/virology , Leukocytes, Mononuclear/virology , Polymerase Chain Reaction , RNA, Viral/genetics , Sequence AlignmentABSTRACT
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/geneticsABSTRACT
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 , GenotypeABSTRACT
Objective: To investigate the effects of hepatitis B virus (HBV) genotype and mutations on the development of hepatocellular carcinoma (HCC) and to establish a new qualified HCC risk scores. Methods: A cohort study enrolling patients with chronic HBV infection was conducted. HBV genotypes were identified by nested multiplex PCR. HBV mutations in the basic core promoter region and PreS region were sequenced after PCR amplification. Scores on risk factors were set based on nomogram. Results: Totally, 1 525 patients were followed-up in this research. A total of 1 110 patients infected with genotype C were followed-up for 8.52 (Q(R): 5.36-11.68) years on average, of whom the incidence of HCC was 11.93/1 000 person-years. In genotype C HBV infected patients, male gender, aged 40 years and over, and four DNA mutations (T1674CG, A1762T/G1764A, A3120T, and A2962G) can increase the risk of HCC (P<0.05); interferon therapy can reduce the risk of HCC (P<0.05). A new HCC predicting model was established according to the results. After validation, the predicted disease-free survival rate was consistent with the real one. Conclusions: Hepatitis B virus genotypes and mutations were closely associated with HCC. The new risk scoring system can well predict HCC occurrence in genotype C HBV infected patients.
Subject(s)
Adult , Aged , Female , Humans , Male , Middle Aged , Carcinoma, Hepatocellular/virology , China/epidemiology , Cohort Studies , DNA, Viral/genetics , Genotype , Hepatitis B virus/genetics , Hepatitis B, Chronic/complications , Liver Neoplasms/virology , Mutation , Predictive Value of Tests , Risk Factors , Sensitivity and SpecificityABSTRACT
Resumen Introducción. La composición genética del huésped determina, entre otros aspectos, el perfil clínico del dengue, lo cual se debería al efecto de variantes en los genes que codifican citocinas proinflamatorias. Objetivo. Evaluar la asociación entre las variantes de tres polimorfismos en los genes candidatos TNFA, IL6 e IFNG con la gravedad del dengue en una población colombiana. Materiales y métodos. Se evaluaron los polimorfismos rs1800750, rs2069843 y rs2069705 de los genes TNFA, IL6 e IFNG, respectivamente, en 226 pacientes con dengue. Los genotipos se tipificaron usando la reacción en cadena de la polimerasa (PCR) y los polimorfismos de la longitud de los fragmentos de restricción (Restriction Fragment Length Polymorphism, RFLP). Para determinar el riesgo de diferentes fenotipos del dengue, se compararon las frecuencias alélicas con la prueba de ji al cuadrado, y los genotipos y los haplotipos, con regresión logística. Por último, los análisis se ajustaron utilizando datos de autoidentificación o del componente genético ancestral. Resultados. El alelo A del rs2069843, ajustado por autoidentificación, se asoció con casos de dengue hemorrágico en afrocolombianos. En la muestra completa, dicho polimorfismo, ajustado por componente genético ancestral, fue reproducible. Además, hubo asociaciones significativas entre las combinaciones alélicas GGT y GAC de los rs1800750, rs2069843 y rs2069705 en pacientes con dengue hemorrágico, con ajuste por componente genético ancestral y sin él. Además, la combinación alélica AGC produjo 58,03 pg/ml más de interleucina 6 que la GGC, independientemente de los componentes genéticos europeo, amerindio y africano. Conclusión. Las variantes de los polimorfismos GGT y GAC de los rs1800750, rs2069843 y rs2069705 en los genes TNFA, IL6 e IFNG, respectivamente, se correlacionaron con la gravedad del dengue en esta muestra de población colombiana.
Abstract Introduction: The genetic makeup of the host contributes to the clinical profile of dengue. This could be due to the effect of variants in the genes encoding pro-inflammatory cytokines. Objective: To evaluate the association between the variants of three polymorphisms in TNFA, IL6 and IFNG candidate genes with dengue severity in a sample of Colombian population. Materials and methods: We evaluated the rs1800750, rs2069843, and rs2069705 polymorphisms in TNFA, IL6 and IFNG candidate genes, respectively, in 226 patients with dengue infection. The genotypes were typed using both polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP). To determine the risk of different dengue phenotypes, we compared allele frequencies with chisquare and genotypes and haplotypes using logistic regression. Finally, these analyzes were adjusted with data from self-identification or the ancestral genetic component. Results: The A allele in the rs2069843 polymorphism, adjusted by self-identification, was associated with dengue hemorrhagic fever cases in Afro-Colombians. In the entire sample, this polymorphism, adjusted by the ancestral genetic component, was reproducible. In addition, there were significant associations between GGT and GAC allelic combinations of rs1800750, rs2069843, and rs2069705 in dengue hemorrhagic fever patients, with and without adjustment by ancestral genetic component. Additionally, the AGC allelic combination produced 58.03 pg/ml of interleukin-6 more than the GGC combination, regardless of European, Amerindian and African genetic components. Conclusions: The variants of GGT and GAC polymorphisms of rs1800750, rs2069843, and rs2069705 in the TNFA, IL6 and IFNG genes, respectively, were correlated with the susceptibility to dengue severity in a sample of Colombian population.
Subject(s)
Adolescent , Adult , Child , Female , Humans , Male , Middle Aged , Young Adult , Interleukin-6/genetics , Interferon-gamma/genetics , Tumor Necrosis Factor-alpha/genetics , Polymorphism, Single Nucleotide , Dengue/genetics , Polymorphism, Restriction Fragment Length , DNA, Viral/genetics , Ethnicity/genetics , Polymerase Chain Reaction , Risk , Cross-Sectional Studies , Prospective Studies , Colombia/epidemiology , Genetic Predisposition to Disease , Dengue/epidemiology , Dengue Virus/classification , Dengue Virus/genetics , Alleles , Genetic Association Studies , Gene Frequency , GenotypeABSTRACT
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/microbiologyABSTRACT
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.