Positive selection results in frequent reversible amino acid replacements in the G protein gene of human respiratory syncytial virus

Human respiratory syncytial virus (HRSV) is the major cause of lower respiratory tract infections in children under 5 years of age and the elderly, causing annual disease outbreaks during the fall and winter. Multiple lineages of the HRSVA and HRSVB serotypes co-circulate within a single outbreak and display a strongly temporal pattern of genetic variation, with a replacement of dominant genotypes occurring during consecutive years. In the present study we utilized phylogenetic methods to detect and map sites subject to adaptive evolution in the G protein of HRSVA and HRSVB. A total of 29 and 23 amino acid sites were found to be putatively positively selected in HRSVA and HRSVB, respectively. Several of these sites defined genotypes and lineages within genotypes in both groups, and correlated well with epitopes previously described in group A. Remarkably, 18 of these positively selected tended to revert in time to a previous codon state, producing a flipflop phylogenetic pattern. Such frequent evolutionary reversals in HRSV are indicative of a combination of frequent positive selection, reflecting the changing immune status of the human population, and a limited repertoire of functionally viable amino acids at specific amino acid sites.

Araçatuba virus: A vaccinialike virus associated with infection in humans and cattle

We describe a vaccinialike virus, Araçatuba virus, associated with a cowpoxlike outbreak in a dairy herd and a related case of human infection. Diagnosis was based on virus growth characteristics, electron microscopy, and molecular biology techniques. Molecular characterization of the virus was done by using polymerase chain reaction amplification, cloning, and DNA sequencing of conserved orthopoxvirus genes such as the vaccinia growth factor (VGF), thymidine kinase (TK), and hemagglutinin. We used VGF-homologous and TK gene nucleotide sequences to construct a phylogenetic tree for comparison with other poxviruses. Gene sequences showed 99% homology with vaccinia virus genes and were clustered together with the isolated virus in the phylogenetic tree. Araçatuba virus is very similar to Cantagalo virus, showing the same signature deletion in the gene. Araçatuba virus could be a novel vaccinialike virus or could represent the spread of Cantagalo virus.

Molecular typing of IberoAmerican Cryptococcus neoformans isolates

A network was established to acquire basic knowledge of Cryptococcus neoformans in IberoAmerican countries. To this effect, 340 clinical, veterinary, and environmental isolates from Argentina, Brazil, Chile, Colombia, Mexico, Peru, Venezuela, Guatemala, and Spain were typed by using M13 polymerase chain reaction-fingerprinting and orotidine monophosphate pyrophosphorylase (URA5) gene restriction fragment length polymorphsm analysis with Hhal and Sau961 in a double digest. Both techniques grouped all isolates into eight previously established molecular types. The majority of the isolates, 68.2% (n=232), were VNI (var. grubii, serotype A), which accords with the fact that this variety causes most human cryptococcal infections worldwide. A smaller proportion, 5.6% (n=19), were VNII (var. grubii, serotype A); 4.1% (n=14), VNIII (AD hybrid), with 9 isolates having a polymorphism in the URA5 gene; 1.8% (n=6), VNIV (var. neoformans, serotype D); 3.5% (n=12), VGI; 6.2% (n=21), VGII; 9.1% (n=31), VGIII, and 1.5% (n=5) VGIV, with all four VG types containing var. gattii serotypes B and C isolates.

Clonagem e expressão da glicoproteína transmembrana do retrovírus HTLV-1 em células de mamíferos

The retrovirus HTLV-1 is the etiological agent of the adult T-cell leukemia and HTLV-1 associated myelopathy/tropical spastic paraparesis. The proviral genome has 9,032 base pairs, showing regulatory and structural genes. The env gene encodes for the transmembrane glycoprotein gp 21. The development of methodologies for heterologous protein expression, as well as the acquisition of a cellular line that constituently expresses the recombinant, were the main goals of this work. The DNA fragment that encodes for gp 21 was amplified by nested-PCR and cloned into a pCR2.1-TOPO vector. After which, a sub-cloning was realized using the expressing vector pcDNA3.1+. The transfection of mammalian cells HEK 293 was performed transitorily and permanently. Production of the recombinant gp 21 was confirmed by flux cytometry experiments and the cell line producing protein will be used in immunogenicity assays.

Clonagem e expressão da glicoproteína transmembrana do vírus linfotrópico de células T humanas em sistema procarioto

HTLV-1 is the virus that causes T cell lymphoma/leukemia in adults and a neurological disorder known as HTLV-associated myelopathy or tropical spastic paraparesis. One of the transmission means is through contaminated blood and its byproducts. Because of the risk of HTLV-associated infections, screening for HTLV was introduced for Brazilian blood donors in 1993. Most of the diagnostic kits used in the national blood banks are bought from foreign companies. Brazil does not have the technology to produce this material and there is a need to produce diagnostic systems with national technology. In this study, we show the expression of gp21/HTLV-1 in Escherichia coli and its reactivity towards monoclonal antibodies and the antibodies of infected patients. Expressing these proteins is the first step towards obtaining diagnostic kits with Brazilian biotechnology.

Avaliação do perfil lipídico entre indivíduos com hepatite C

Metabolic profiles correlate with hepatitis C virus (HCV) infection and are prognostic for the viral response. However, little is known about the association between lipid profiles and viral load in chronic patients carrying HCV genotypes 1, 2 and 3. The aim of this study was to investigate the influence of the viremia and viral genotype on lipid metabolism by observing the variations in serum lipoprotein and apolipoprotein B, to assess whether HCV predisposes individuals to lipid imbalance and favors the appearance of vascular complications. A sample group of 150 chronic HCV patients with viral genotypes 1, 2 or 3 and a control group of 20 healthy adults (10 men and 10 women), all aged from 20 to 50 years were studied. The serum lipid profile of the chronic patients was analyzed and compared to that of the control group. The high-density lipoprotein (HDL), very low-density lipoprotein (VLDL) and triglyceride levels of the sample group were lower than those of the control group, while the low-density lipoprotein (LDL) and apolipoprotein B levels of the patients were higher. These differences were more significant in patients carrying genotype 3a. There was a positive correlation between the viremia and the changes in apolipoprotein B levels in patients carrying genotype 1b. It was inferred that the risk of developing vascular complications raised in HCV patients. As 90% of LDL protein is composed of apolipoprotein B, the plasmatic concentration of the latter indicates the number of potentially atherogenic particles. Therefore, the lipid profile monitoring may aid in the diagnosis of hepatic infection severity and equally act as a good prognostic marker.

Caracterização do gene da proteína capsidial do Grapevine virus A em videiras afetadas pela acanaladura do lenho de Kober no Estado de São Paulo

O presente trabalho caracteriza o gene codificador da proteína capsidial do isolado do Grapevine virus A (GVA) encontrado no Estado de São Paulo (GVA-SP). RNA total foi extraído de folhas e pecíolos de plantas de videira (Vitis spp.) da variedade 'Kober 5BB' e submetido a RT-PCR usando oligonucleotídeos desenhados para amplificar um fragmento entre as posições 6409 e 7175 do RNA do GVA (GenBank, acesso X75433). Foi obtido um fragmento de tamanho esperado (767 nt) que inclui o gene da proteína capsidial, codificando 198 aminoácidos. A seqüência do GVA-SP apresentou similaridade de nucleotídeos e aminoácidos de, respectivamente, 86-92,3% e 94,5-98% com isolados do GVA da Europa, África e Japão (Acessos X75433, AF441234, AF007415, AB039841) e da região Sul do Brasil (Acesso AF494187), sendo, entretanto, mais similar aos isolados africano e italiano.

Caracterização do gene da proteína capsidial de dois isolados, patologicamente distintos e sorologicamente semelhantes, do Grapevine virus B em videiras no Estado de São Paulo

No presente trabalho, descreve-se a caracterização do gene codificador da proteína capsidial de dois isolados sintomatologicamente distintos do Grapevine virus B (GVB). Para isto, RNA totais foram extraídos de folhas e pecíolos de videiras (Vitis spp.) infetadas, cultivares Rubi (GVB-C SP) e Itália (GVB-I SP) e utilizados para amplificar, por RT/PCR, um fragmento entre as posições 6425 e 7118 (694 nucleotídeos, nt) do RNA do GVB (GenBank, acesso X75448). O fragmento obtido inclui o gene da proteína capsidial (594 nt) codificando 197 aminoácidos com massa molecular estimada em aproximadamente 21.600 Da. A seqüência do GVB-C SP apresentou maior similaridade de nucleotídeos e aminoácidos deduzidos com o isolado italiano (acesso X75448), enquanto que o GVB-I SP foi mais similar a um outro isolado brasileiro do GVB descrito no Rio Grande do Sul (GVB BR1, acesso AF438410). Os dois isolados paulistas do GVB podem ser diferenciados por digestão com a enzima de restrição EcoRI, uma vez que há um sítio interno no GVB-C SP que está ausente no isolado GVB-I SP.

Genetic grouping of avian infectious bronchitis virus isolated in Brazil based on RT-PCR/RFLP analysis of the S1 gene

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Deletion of Epstein-Barr virus latent membrane protein 1 gene in United States and Brazilian Hodgkin's disease and reactive lymphoid tissue: High frequency of a 30-bp deletion

A 30-basepair (bp) deletion in the Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1) gene has been reported in nasopharyngeal carcinoma and EBV-associated malignant lymphomas. Prior studies have found the deletion in about 10% to 28% of cases of Hodgkin's disease (HD), particularly in cases with aggressive histology. We studied the prevalence of 30-bp LMP1 gene deletion in EBV-positive HD in the United States (US) (12 cases) and Brazil (26 cases) with comparison to reactive lymphoid tissues (21 cases) and HD without EBV-positive Reed-Sternberg cells (15 cases). We studied the status of the LMP1 gene by Southern blot hybridization of polymerase chain reaction (PCR) products obtained after amplification with primers spanning the site of the deletion. We also performed EBV typing, EBER1 in situ hybridization, and LMP1 protein immunohistochemistry. EBV was detected in 12/26 (46%) cases of HD from the US and 26/27 (96%) cases of Brazilian HD. The 30-bp LMP1 gene deletion was observed in 4/12 (33%) cases of EBV-positive HD from US, and 12/26 (46%) cases of Brazilian EBV-positive HD, including 3 cases of type B EBV, as compared with 12/21 (57%) reactive lymphoid tissues and 9/15 (60%) cases of EBV-negative HD. US and Brazilian HD showed a higher prevalence of the 30-bp LMP1 gene deletion, compared with studies of others. The unexpected finding of high incidence of 30-bp deletion in LMP1 gene in reactive lymphoid tissue and HD without EBV-positive Reed-Sternberg cells suggests that this deletion may not be relevant to HD pathogenesis in most cases. Copyright (C) 1997 by W.B. Saunders Company.

Epstein-barr virus infection and single nucleotide Polymorphisms in the promoter region of interleukin 10 gene in patients with Hodgkin lymphoma

Context. - Hodgkin lymphoma is a neoplastic disease in which the immune system plays a major role in its pathogenesis. Interleukin 10 ( IL-10), an immunosuppressive cytokine actively produced in patients with Hodgkin lymphomas, favors the survival of the Hodgkin/Reed-Sternberg cells. Individual variations in IL-10 levels may be due, in part, to the presence of single nucleotide polymorphisms in the IL10 gene promoter.Objective. - To evaluate whether particular single nucleotide polymorphisms in the IL10 gene are found more frequently in Hodgkin lymphoma cases associated with Epstein-Barr virus infection.Design. - the identification of single nucleotide polymorphisms at positions -1082 and -819/-592 in the IL10 gene was performed by polymerase chain reaction and restriction length fragment polymorphisms analysis in 65 cases of Hodgkin lymphoma and 50 cases of reactive benign follicular lymphoid hyperplasia ( non-Hodgkin lymphoma control group).Results. - the frequency of the genotype GG at position -1082 was found to be significantly higher in patients with Epstein-Barr virus-positive Hodgkin lymphoma compared with Epstein-Barr virus-negative cases.Conclusions. - the results suggest that the presence of specific single nucleotide polymorphisms in the IL10 gene, notably those associated with high IL-10 production, may play a role in the susceptibility to Epstein-Barr virus -positive Hodgkin lymphoma development.

Genotyping of Epstein-Barr virus in Brazilian Burkitt's lymphoma and reactive lymphoid tissue - Type A with a high prevalence of deletions within the latent membrane protein gene

Both Epstein-Barr virus (EBV) types A and B are found in endemic Burkitt's lymphoma (BL) occurring in equatorial Africa. We studied 17 cases of Brazilian BL previously demonstrated to be EBV-positive to determine the EBV type as well as the presence of a characteristic 30 bp deletion within the 3' end of the latent membrane protein-1 (LMP-1) gene that may be important to the pathogenesis of several EBV-associated neoplasms. All case in which the age was known were children. We found type A EBV in 13 of 14 (93%) evaluable cases, and type B in one case. The LMP-1 deletion was found in 12 of 15 (80%) evaluable cases, including the one case of type B EBV, and a similar high prevalence (59%) of the deletion was detected in EBV-positive normal and reactive lymphoid tissues from individuals from the same geographic region. The high proportion of cases associated with type A EBV suggests that immunodeficiency is not an important factor in the pathogenesis of Brazilian BL, in contrast to endemic African BL. The presence of the LMP-1 deletion in a high prevalence in the normal population in this region is unexplained.

Impact of Epstein-Barr virus load, virus genotype, and frequency of the 30bp deletion in the viral BNLF-1 gene in patients harboring the human immunodeficiency virus

Patients infected with the human immunodeficiency virus (HIV) are at higher risk of developing Epstein-Barr Virus (EBV)-associated lymphomas. The usefulness of monitoring EBV in peripheral blood mononuclear cells (PBMCs) of patients infected with HIV has not been established. The aim of this study was to evaluate the EBV viral load in PBMCs, the frequency of viral genotypes, and the presence of the 30-bp deletion in the BNLF-1 gene. DNA samples from 156 patients attending the HIV/AIDS Day Clinic at Botucatu School of Medicine, Sao Paulo State University were evaluated. The EBV viral load was detectable by real time PCR in 123/156 (78.8%) cases and was higher in patients not receiving antiretroviral treatment or under therapeutic failure than in patients under successful highly active antiretroviral therapy (HAART) (P=0.0076). Overall, the profile of patients with high EBV viral load included elevated HIV viremia (P=0.0005), longer time of HIV diagnosis (P=0.0026), and increased levels of T CD8 + lymphocytes (P=0.0159). The successful amplification of the EBNA-2 gene by nested-PCR was achieved in 95 of 123 (77.2%) cases, of which 75.8% were EBV-1, 9.5% EBV-2, and 14.7% were co-infected with both EBV-1 and -2. The analysis of the BNLF-1 gene was possible in 99 of 123 (80.5%) cases, of which 50.5% had the 30-bp deletion. EBV-1 was more common than EBV-2, which may reflect the fact that the cohort was predominantly Caucasian and heterosexual. J. Med. Virol. 85:2110-2118, 2013. © 2013 Wiley Periodicals, Inc.

Infectious bronchitis virus: detection and vaccine Strain differentiation by semi-nested RT-PCR

A semi-nested reverse transcription-polymerase chain reaction (Semi-N-RT-PCR) was developed and used to detect the S glycoprotein gene of infectious bronchitis virus (IBV) strains and to discriminate H120 vaccine strain from other strains. Viral RNA was extracted from the allantoic fluid of chicken embryos and from tissues of chickens experimentally infected with different strains of IBV. Amplification and identification of the viral RNA was performed using two sets of primers complementary to a region of the S glycoprotein gene in the Semi-N-RT-PCR assay. The pair of primers used in the first PCR consisted of universal oligonucleotides flanking a more variable region of S1-S2 gene. The second primer pair was used in the Semi-N-RT-PCR and was comprised of one of the primers from the first universal pair together with either another universal internal oligolucleotide or a oligonucleotide sequence specific for the H120 strain of IBV. The universal primers detected all reference IBV strains and field isolates tested herein. The Semi-N-RT-PCR had high sensitivity and specificity, and was able to differentiate the H120 vaccine strain from other reference IBV strains; including M41 strain. All tissue samples collected from chickens experimentally infected with H120 or M41 strains were positive in the semi-nested RT-PCR using universal primers, while only the H120-infected tissue samples were amplified by the set of primers containing the H120-oligonucleotide. In conclusion, the ability of Semi-N-RT-PCR to detect distinct IBV strains and preliminarily discriminate the vaccine strain (H120) closes a diagnostic gap and offers the opportunity to use comprehensive PCR procedures for the IBV diagnosis.