An overview of Zika virus genotypes and their infectivity

ABSTRACT Zika virus (ZIKV) is an enveloped, single-stranded RNA arbovirus belonging to the genus Flavivirus. It was first isolated from a sentinel monkey in Uganda in 1947. More recently, ZIKV has undergone rapid geographic expansion and has been responsible for outbreaks in Southeast Asia, the Pacific Islands, and America. In this review, we have highlighted the influence of viral genetic variants on ZIKV pathogenesis. Two major ZIKV genotypes (African and Asian) have been identified. The Asian genotype is subdivided into Southwest Asia, Pacific Island, and American strains, and is responsible for most outbreaks. Non-synonymous mutations in ZIKV proteins C, prM, E, NS1, NS2A, NS2B, NS3, and NS4B were found to have a higher prevalence and association with virulent strains of the Asian genotype. Consequently, the Asian genotype appears to have acquired higher cellular permissiveness, tissue persistence, and viral tropism in human neural cells. Therefore, mutations in specific coding regions of the Asian genotype may enhance ZIKV infectivity. Considering that mutations in the genomes of emerging viruses may lead to new virulent variants in humans, there is a potential for the re-emergence of new ZIKV cases in the future.

Antiretroviral therapy immunologic non-response in a Brazilian population: association study using pharmaco- and immunogenetic markers

ABSTRACT Background: Antiretroviral therapy (ART) saved millions from HIV-1 infection and AIDS, but some patients do not experience adequate CD4+ T cells gain despite achieving viral suppression. The genetic component of this condition is not yet completely elucidated. Objective: To identify predictive genetic markers of immune response to ART. Methods: Case-control study. Out of 176 HIV-infected patients recruited in the city of Recife, Northeast Brazil, 67 patients with no immunologic response were the cases and the remaining 109 patients who responded were the controls. A set of 94 selected single nucleotide polymorphisms (SNPs) involved in antiretroviral drugs pharmacodynamic pathways and immune system homeostasis were genotyped, while the remaining 48 were ancestry informative markers (AIMs) for controlling for eventual hidden population structure. Results: Male patients were overrepresented in non-responder group (p = 0.01). Non-responders also started with lower absolute CD4+ T cell counts (p < 0.001). We found five SNPs significantly associated with the outcome, being three more frequent in non-responders than responders: rs2243250 (IL4) A allele (p = 0.04), rs1128503 (ABCB1) A allele (p = 0.03) and rs707265 (CYP2B6) A allele (p = 0.02), whereas the other two were less frequent in non-responders: rs2069762 (IL2) C allele (p = 0.004) and rs4646437 (CYP3A4) A allele (p = 0.04). Conclusion: Some significant univariate associations remained independently associated at multivariate survival analysis modeling, such as pre-treatment CD4+ T cells counts, IL2 and ABCB1 genotypes, and use of protease inhibitors, yielding a predictive model for the probability for immune response. More studies are needed to unravel the genetic basis of ART immunological non-response.

DEFB1 gene polymorphisms and tuberculosis in a Northeastern Brazilian population

Abstract β-Defensin-1, an antimicrobial peptide encoded by the DEFB1 gene, is known to play an important role in lung mucosal immunity. In our association study we analyzed three DEFB1 functional polymorphisms -52G>A (rs1799946), -44C>G (rs1800972) and -20G>A (rs11362) in 92 tuberculosis patients and 286 healthy controls, both from Northeast Brazil: no association was found between the studied DEFB1 polymorphisms and the disease. However we cannot exclude that this lack of association could be due to the low number of subjects analyzed, as suggested by the low statistical power achieved for the three analyzed SNPs (values between 0.16 and 0.50).

NLRP3 polymorphism is associated with protection against human T-lymphotropic virus 1 infection

Inter-individual heterogeneity in the response to human T-lymphotropic virus 1 (HTLV-1) infection has been partially attributed to host genetic background. The antiviral activity of the inflammasome cytoplasmic complex recognises viral molecular patterns and regulates immune responses via the activation of interleukin (IL)-1 family (IL-1, IL-18 and IL-33) members. The association between polymorphisms in the inflammasome receptors NLRP1 and NLRP3 and HTLV-1 infection was evaluated in a northeastern Brazilian population (84 HTLV-1 carriers and 155 healthy controls). NLRP3 rs10754558 G/G was associated with protection against HTLV-1 infection (p = 0.012; odds ratio = 0.37). rs10754558 affects NLRP3 mRNA stability; therefore, our results suggest that higher NLRP3 expression may augment first-line defences, leading to the effective protection against HTLV-1 infection.

Fequency distribution of HLA DQ2 and DQ8 in celiac patients and first-degree relatives in Recife, northeastern Brazil

AIMS: The aim of this study was to evaluate the frequencies of the HLA genotypes DQ2 and DQ8 and the alleles A1*05, A1*0201, B1*0201 and B1*0302 in individuals with celiac disease in Recife, northeastern Brazil. METHODS: HLA DQ2 and DQ8 genotyping was performed for 73 individuals with celiac disease and 126 first-degree relatives with negative transglutaminase serology. The alleles DQA1*05, DQA1*0201, DQB1*02 and DQB1*0302 were identified by sequencing using specific primers and the EU-DQ kit from the Eurospital Laboratory, Trieste, Italy and double-checked by the All Set SPP kit (Dynal). RESULTS: Among the 73 cases, 50 (68.5 percent) had the genotype DQ2, 13 (17.8 percent) had DQ8, 5 (6.8 percent) had DQ2 and DQ8, and 5 did not have any of these genotypes. Among the 5 negative individuals, four had the B1*02 allele and one did not have any of the alleles studied. B1*02 was the most frequent allele in both groups (94 percent in the patients and 89 percent in the control relatives). CONCLUSIONS: In this study, celiac disease was associated with the genotypes DQ2 and DQ8. DQ2 predominated, but the distribution of the frequencies was different from what has been found in European populations and was closer to what has been found in the Americas. The high frequencies of the HLA genotypes DQ2 and DQ8 that were found in first-degree relatives would make it difficult to use these HLA genotypes for routine diagnosis of celiac disease in this group.

Principles and applications of polymerase chain reaction in medical diagnostic fields: a review: [revision] / Princípios e aplicações da reação em cadeia de Polimerase em áreas médicas diagnósticas: uma revisão: [revisão]

Recent developments in molecular methods have revolutionized the detection and characterization of microorganisms in a broad range of medical diagnostic fields, including virology, mycology, parasitology, microbiology and dentistry. Among these methods, Polymerase Chain Reaction (PCR) has generated great benefits and allowed scientific advancements. PCR is an excellent technique for the rapid detection of pathogens, including those difficult to culture. Along with conventional PCR techniques, Real-Time PCR has emerged as a technological innovation and is playing an ever-increasing role in clinical diagnostics and research laboratories. Due to its capacity to generate both qualitative and quantitative results, Real-Time PCR is considered a fast and accurate platform. The aim of the present literature review is to explore the clinical usefulness and potential of both conventional PCR and Real-Time PCR assays in diverse medical fields, addressing its main uses and advances.

O advento dos métodos moleculares tem, nos últimos anos, revolucionado a detecção e caracterização dos microorganismos em diversas áreas médicas diagnósticas, tais como virologia, micologia, parasitologia, microbiologia e odontologia. Dentre as técnicas baseadas em biologia molecular, a PCR (Polymerase Chain Reaction) trouxe enormes benefícios e desenvolvimentos científicos, se mostrando como um excelente caminho para a rápida detecção de patógenos, até mesmo aqueles de difícil cultivo. Derivada da PCR convencional, a PCR em Tempo Real se mostra como uma inovação tecnológica e vem conquistando espaço nos diagnósticos clínicos e nos laboratórios de pesquisa por apresentar a capacidade de gerar, além de resultados qualitativos, resultados quantitativos, se mostrando de forma mais rápida e precisa. Este trabalho de revisão tem por objetivo explorar a utilidade clínica da técnica de PCR convencional e em Tempo real nas diversas áreas médicas supracitadas, abrangendo seus principais usos e avanços, direcionando para o cotidiano profissional.

Evaluation of real time PCR technique to diagnosis of human T-lymphotropic virus type I (HTLV-I) in patients in the Hematologia da Fundação Hemope Hospital, in Northeastern Brazil / Avaliação da técnica de PCR em tempo real para o diagnóstico do virus linfotrópico tipo I de células T humana (HTLV-I) em pacientes do Hospital de Hematologia da Fundação Hemope, no Nordeste do Brasil

As a high degree of homology exists between the proviral genomes of HTLV-I and HTLV-II, there is significant cross-reactivity. Therefore although detection of HTLV antibodies is characteristic of viral infection, it is not sufficient to confirm the presence of the viral type. Molecular tests used to diagnose the HTLV-I/II viruses are based oninvestigations of proviral genomic sequences, and allow for an infection to be diagnosed prior to the appearance of any sign or symptom. The HTLV proviral load in infected individuals can be determined using real-time PCR, a faster method with less risk of contamination than simple or nested PCR. We analyzed 63 samples from the Hemope Hospital, of which 33 were from HTLV seropositive individuals and 30 from blood donors, to determine the type of virus and the proviral load. The sensitivity of qualitative PCR in comparison to ELISA was 87.5% (95% IC: 70.1 - 95.9%) and the specificitywas 100% (IC 95%: 85.9 - 100.0%). The sensitivity and specificity of real-time PCR in comparison to the serological test (ELISA) were 100% (95% IC: 86.7 - 100.0%) and 96.67% (95% IC: 80.9 - 99.8%) respectively. The proviral load in the seropositiveindividuals ranged from 13 to 343820 copies/106 PBMC cells. Our study also observed that individuals with TSP/HAM had a higher proviral load than those who showed no symptoms. The use of real time PCR for routine clinical testing of infected individuals will play a significant role in identifying the virus type and determining the proviral load, thereby providing more appropriate treatment.

Como os genomas provirais do HTLV-I e HTLV-II exibem grande homologia, há uma expressiva sororeatividade cruzada. Assim, a detecção de anticorpos anti-HTLV-I/II embora caracterize infecção viral, não permite estabelecer distinção entre os agentes. Os testes moleculares empregados para o diagnóstico dos vírus HTLV-I/II, baseiam-se na pesquisa de seqüências genômicas provirais permitindo o diagnóstico da infecção antes de aparecer sinal ou sintoma. A carga proviral de HTLV pode ser determinadaatravés da utilização da PCR em tempo real, uma técnica rápida e com menor risco de contaminação que a PCR simples ou nested PCR. Analisamos, 63 amostras do Hospital HEMOPE, das quais 33 foram de indivíduos com sorologia reagente para HTLV e 30 de doadores de sangue, para determinar o tipo de vírus e a carga proviral. A sensibilidade da PCR qualitativa emrelação ao ELISA foi de 87,9% (IC 95%: 70,9-96,0%) e a especificidade foi de 100% (IC 95%: 85,9-100,0%). A sensibilidade e especificidade da PCR em tempo real foram de 100% (IC95%: 86,7-100,0%) e 96,67% (IC 95%: 80,9-99,8%), respectivamente.A carga proviral variou entre 13 cópias/106 células PBMC e 343820 cópias/106 células PBMC. Nosso estudo também observou que os indivíduos com PET/MAH tiveram carga proviral mais elevada que a dos indivíduos assintomáticos. A utilização da PCR em tempo real na rotina clínica dos indivíduos infectados poderá desempenhar um papel relevante na identificação do vírus e na determinação da carga proviral, contribuindo para direcionar um tratamento adequado.

Chlamydia infection in patients with and without cervical intra-epithelial lesions tested by real-time PCR vs. direct immunofluorescence

This study compares the detection rates of Chlamydia trachomatis by two techniques, direct immunofluorescence (IMF) and real time polymerase chain reaction (PCR), in patients with and without intra-epithelial cervical lesions (SIL) in Recife. We conducted a transversal study involving 35 women with SIL and 35 without SIL attended at Ambulatório Especializado da Mulher, Recife, Brazil. They were tested for Chlamydia trachomatis using two techniques, direct IMF or real time PCR. The rates of Chlamydia trachomatis detection were compared and the association with intra-epithelial cervical lesions was determined using the chi-square test at a 5 percent level of significance. Concordance between the tests was evaluated using kappa. The global prevalence of Chlamydia infection was 47.1 percent by direct IMF and 58.6 percent by real time PCR. A significant association was observed between Chlamydia diagnosis and presence of intra-epithelial cervical lesions, with about 80 percent positive results by direct IMF and 77.1 percent by real time PCR. However, the detected rate of infection with Chlamydia trachomatis was significantly greater in patients without intra-epithelial cervical lesions tested by real time PCR (40 percent) when compared to direct IMF (14.3 percent). The concordance between the tests was weak, with a kappa coefficient of 0.4. Both real time PCR and direct IMF detected elevated rates of Chlamydia infection in patients with intra-epithelial cervical lesions (80 percent) but the tests were discordant when patients without cervical lesions were tested, possibly because sensitivity of real time PCR is greater.