Alex Olvera

Revisiting the taxonomical classification of Porcine Circovirus type 2 (PCV2): still a real challenge

BackgroundPCV2 has emerged as one of the most devastating viral infections of swine farming, causing a relevant economic impact due to direct losses and control strategies expenses. Epidemiological and experimental studies have evidenced that genetic diversity is potentially affecting the virulence of PVC2. The growing number of PCV2 complete genomes and partial sequences available at GenBank questioned the accepted PCV2 classification.MethodsNine hundred seventy five PCV2 complete genomes and 1,270 ORF2 sequences available from GenBank were subjected to recombination, PASC and phylogenetic analyses and results were used for comparison with previous classification scheme.ResultsThe outcome of these analyses favors the recognition of four genotypes on the basis of ORF2 sequences, namely PCV2a, PCV2b, PCV2c and PCV2d-mPCV2b. To deal with the difficulty of founding an unambiguous classification and accounting the impossibility to define a p-distance cut-off, a set of reference sequences that could be used in further phylogenetic studies for PCV2 genotyping was established. Being aware that extensive phylogenetic analyses are time-consuming and often impracticable during routine diagnostic activity, ORF2 nucleotide positions adequately conserved in the reference sequences were identified and reported to allow a quick genotype differentiation.ConclusionsGlobally, the present work provides an updated scenario of PCV2 genotypes distribution and, based on the limits of the previous classification criteria, proposes new rapid and effective schemes for differentiating the four defined PCV2 genotypes.

Trimeric Autotransporters of Haemophilus parasuis: Generation of an Extensive Passenger Domain Repertoire Specific for Pathogenic Strains

Haemophilus parasuis is the agent responsible for causing Glässers disease, but little is known about the pathogenic determinants of this major pig disease. Here we describe, for the pathogenic strain Nagasaki, the molecular characterization of 13 trimeric autotransporters as assessed by the presence of YadA C-terminal translocator domains which were classified into three groups. All passenger domains possess motifs and repeats characteristic of adhesins, hemagglutinins, and invasins with various centrally located copies of collagen-like repeats. This domain architecture is shared with two trimeric autotransporter proteins of H. somnus 129Pt. Genomic comparison by microarray hybridization demonstrated homologies among H. parasuis virulent strains and high divergence with respect to nonvirulent strains. Therefore, these genes were named vtaA (virulence-associated trimeric autotransporters). The sequencing of 17 homologous vtaA genes of different invasive strains highlighted an extensive mosaic structure. Based also on the presence of DNA uptake signal sequences within the vtaA genes, we propose a mechanism of evolution by which gene duplication and the accumulation of mutations and recombinations, plus the lateral gene transfer of the passenger domain, led to the diversity of this multigene family. This study provides insights to help understand the tissue colonization and invasiveness characteristic of H. parasuis pathogenic strains.

Porcine circovirus type 2 (PCV2) Cap and Rep proteins are involved in the development of cell-mediated immunity upon PCV2 infection.

The aim of the present study was to investigate the role of the capside (Cap) and replicase (Rep) proteins of Porcine circovirus type 2 (PCV2) as well as the whole PCV2 (both PCV2a and PCV2b genotypes) in the induction of cell-mediated immunity upon infection. At 6 weeks of age, six pigs were intranasally inoculated with the Stoon 1010 (Stoon) isolate (PCV2a) and seven with the Sp-7-10-54-13 (Sp) isolate (PCV2b). None of the pigs developed clinical disease but the Sp group had significantly higher proportion of pigs with PCV2-associated lesions and PCV2 load in tissues compared to the Stoon group. In both groups, development of IFN-gamma secreting cells (SC) in response to the whole PCV2 and Cap protein was detected by means of an ELISPOT from day 7 post-inoculation (PI) to the end of the study (21 days PI). Significant responses against Rep protein were only detected in Sp-inoculated pigs. No differences in ELISPOT results were seen when either PCV2a or PCV2b was used in vitro to recall peripheral blood mononuclear cells (PBMC) in any group. Stimulation of PBMC with the whole virus but not with Cap or Rep protein induced IL-10-SC in all pigs regardless of their PCV2 infection status, indicating an innate origin of this response. The results from this study demonstrate that PCV2-infected pigs developed cell-mediated immunity to Cap and Rep proteins and that, in the course of a sub-clinical infection, development and strength of such responses are possibly related to the levels of PCV2 replication.

Immunogenicity and protection against Haemophilus parasuis infection after vaccination with recombinant virulence associated trimeric autotransporters (VtaA)

Haemophilus parasuis is the etiological agent of Glässers disease in swine, characterized by fibrinous polyserositis, polyarthritis and meningitis. The lack of a vaccine against a broad spectrum of strains has limited the control of the disease. Recently, virulence associated trimeric autotransporters (VtaA) were described as antigenic proteins of H. parasuis. In this study 6 VtaA were produced as recombinant proteins and used to immunize snatch-farrowed, colostrum-deprived piglets. Immunized animals developed specific systemic and mucosal antibodies. The protective capacity of the anti-VtaA antibodies was evaluated by the inoculation of 3 × 10(8) or 6 × 10(6) colony forming units (CFU) of the highly virulent strain Nagasaki. Vaccinated animals had a delayed course of disease and 33 or 57%, respectively, of the animals survived the lethal challenge. The partial protection achieved with the recombinant VtaA supports their potential as candidates to be included in future vaccine formulations against H. parasuis.

Uncommon Pathways of Immune Escape Attenuate HIV-1 Integrase Replication Capacity

ABSTRACT An attenuation of the HIV-1 replication capacity (RC) has been observed for immune-mediated escape mutations in Gag restricted by protective HLA alleles. However, the extent to which escape mutations affect other viral proteins during natural infection is not well understood. We generated recombinant viruses encoding plasma HIV-1 RNA integrase sequences from antiretroviral-naïve individuals with early (n = 88) and chronic (n = 304) infections and measured the in vitro RC of each. In contrast to data from previous studies of Gag, we observed little evidence that host HLA allele expression was associated with integrase RC. A modest negative correlation was observed between the number of HLA-B-associated integrase polymorphisms and RC in chronic infection (R = −0.2; P = 0.003); however, this effect was not driven by mutations restricted by protective HLA alleles. Notably, the integrase variants S119R, G163E, and I220L, which represent uncommon polymorphisms associated with HLA-C*05, -A*33, and -B*52, respectively, correlated with lower RC (all q < 0.2). We identified a novel C*05-restricted epitope (HTDNGSNF114–121) that likely contributes to the selection of the S119R variant, the polymorphism most significantly associated with lower RC in patient sequences. An NL4-3 mutant encoding the S119R polymorphism displayed a ∼35%-reduced function that was rescued by a single compensatory mutation of A91E. Together, these data indicate that substantial HLA-driven attenuation of integrase is not a general phenomenon during HIV-1 adaptation to host immunity. However, uncommon polymorphisms selected by HLA alleles that are not conventionally regarded to be protective may be associated with impaired protein function. Vulnerable epitopes in integrase might therefore be considered for future vaccine strategies.

Virulence-associated trimeric autotransporters of Haemophilus parasuis are antigenic proteins expressed in vivo

Glässer’s disease is a re-emerging swine disease characterized by a severe septicaemia. Vaccination has been widely used to control the disease, although there is a lack of extended cross-protection. Trimeric autotransporters, a family of surface exposed proteins implicated in host-pathogen interactions, are good vaccine candidates. Members of this family have been described in Haemophilus parasuis and designated as virulence-associated trimeric autotransporters (VtaA). In this work, we produced 15 recombinant VtaA passenger domains and looked for the presence of antibodies directed against them in immune sera by immunoblotting. After infection with a subclinical dose of H. parasuis Nagasaki, an IgG mediated antibody response against 6 (VtaA1, 5, 6, 8, 9 and 10) of the 13 VtaA of the Nagasaki strain was detected, indicating that they are expressed in vivo. IgA production against VtaA was detected in only one animal. VtaA were more likely to be late antigens when compared to early (Omp P5 and Omp P6) and late (YaeT) defined antigens. Antibody cross-reaction with two orthologs of Nagasaki’s VtaA5 and 6, VtaA15 and 16 of strain HP1319, was also detected. No antibodies against VtaA were detected in the sera of animals immunized with a bacterin of the Nagasaki strain, suggesting poor expression in the in vitro conditions used. Taken together, these results indicate that VtaA are good candidate immunogens that could be used to improve H. parasuis vaccines. However, their capacity to confer protective immunity needs to be further studied.

Identification of potentially virulent strains of Haemophilus parasuis using a multiplex PCR for virulence-associated autotransporters (vtaA)

Haemophilus parasuis is the aetiological agent of Glässers disease and is also a commensal of the upper respiratory tract of pigs. Trimeric autotransporter (vtaA) genes have been identified in H. parasuis and divided into three groups on the basis of the translocator domain sequence. In this study, group 3 vtaA genes were demonstrated by PCR in all 157 H. parasuis isolates tested. Group 1 vtaA genes were associated with virulent strains; 52/54 (96%) group 1 vtaA negative field isolates were isolated from the nasal passages of healthy animals, whereas no group 1 vtaA negative field isolates were isolated from cases of Glässers disease. There was an association between absence of group 1 vtaA, sensitivity to phagocytosis and serum and classification of isolates into nasal cluster C by multilocus sequence typing. A multiplex PCR was developed for diagnosis of H. parasuis at the species level (group 3 vtaA positive) and to differentiate putative non-virulent strains (group 1 vtaA negative). When applied to field samples, the PCR confirmed a high prevalence of H. parasuis in conventionally farmed pigs and demonstrated that almost half of the animals carried potentially virulent strains.

Direct Interrogation of Viral Peptides Presented by the Class I HLA of HIV-Infected T Cells

ABSTRACT Identification of CD8+ cytotoxic T lymphocyte (CTL) epitopes has traditionally relied upon testing of overlapping peptide libraries for their reactivity with T cells in vitro. Here, we pursued deep ligand sequencing (DLS) as an alternative method of directly identifying those ligands that are epitopes presented to CTLs by the class I human leukocyte antigens (HLA) of infected cells. Soluble class I HLA-A*11:01 (sHLA) was gathered from HIV-1 NL4-3-infected human CD4+ SUP-T1 cells. HLA-A*11:01 harvested from infected cells was immunoaffinity purified and acid boiled to release heavy and light chains from peptide ligands that were then recovered by size-exclusion filtration. The ligands were first fractionated by high-pH high-pressure liquid chromatography and then subjected to separation by nano-liquid chromatography (nano-LC)–mass spectrometry (MS) at low pH. Approximately 10 million ions were selected for sequencing by tandem mass spectrometry (MS/MS). HLA-A*11:01 ligand sequences were determined with PEAKS software and confirmed by comparison to spectra generated from synthetic peptides. DLS identified 42 viral ligands presented by HLA-A*11:01, and 37 of these were previously undetected. These data demonstrate that (i) HIV-1 Gag and Nef are extensively sampled, (ii) ligand length variants are prevalent, particularly within Gag and Nef hot spots where ligand sequences overlap, (iii) noncanonical ligands are T cell reactive, and (iv) HIV-1 ligands are derived from de novo synthesis rather than endocytic sampling. Next-generation immunotherapies must factor these nascent HIV-1 ligand length variants and the finding that CTL-reactive epitopes may be absent during infection of CD4+ T cells into strategies designed to enhance T cell immunity. IMPORTANCE HIV-1 epitopes catalogued by the Los Alamos National Laboratory (LANL) have yielded limited success in vaccine trials. Because the HLA of infected cells have not previously been assessed for HIV-1 ligands, the objective here was to directly characterize the viral ligands that mark infected cells. Recovery of HLA-presented peptides from HIV-1-infected CD4+ T cells and interrogation of the peptide cargo by mass spectrometric DLS show that typical and atypical viral ligands are efficiently presented by HLA and targeted by human CTLs. Nef and Gag ligands dominate the infected cells antigenic profile, largely due to extensive ligand sampling from select hot spots within these viral proteins. Also, HIV-1 ligands are often longer than expected, and these length variants are quite antigenic. These findings emphasize that an HLA-based view of HIV-1 ligand presentation to CTLs provides previously unrealized information that may enhance the development of immune therapies and vaccines.

Applying phylogenetic analysis to viral livestock diseases: moving beyond molecular typing.

Changes in livestock production systems in recent years have altered the presentation of many diseases resulting in the need for more sophisticated control measures. At the same time, new molecular assays have been developed to support the diagnosis of animal viral disease. Nucleotide sequences generated by these diagnostic techniques can be used in phylogenetic analysis to infer phenotypes by sequence homology and to perform molecular epidemiology studies. In this review, some key elements of phylogenetic analysis are highlighted, such as the selection of the appropriate neutral phylogenetic marker, the proper phylogenetic method and different techniques to test the reliability of the resulting tree. Examples are given of current and future applications of phylogenetic reconstructions in viral livestock diseases.

Evaluation of cell-mediated immune responses against porcine circovirus type 2 (PCV2) Cap and Rep proteins after vaccination with a commercial PCV2 sub-unit vaccine.

This study investigated the development of cellular immunity to Porcine circovirus type 2 (PCV2) Cap and Rep proteins in pigs vaccinated with a commercial PCV2 genotype a (PCV2a) based sub-unit vaccine, before and after a heterologous challenge with a PCV2b isolate. At three weeks of age, 20 pigs were inoculated intramuscularly with either the vaccine product (V group, n=9) or phosphate buffered saline solution (PBS) (NV group, n=11). Three weeks after vaccination, pigs were challenged intranasally with PCV2b (V-C and NV-C groups) or PBS (V-NC and NV-NC groups). None of the pigs developed clinical signs during the whole experiment, but all NV-C and 3/5 V-C pigs developed viraemia. Vaccination induced the development IFN-γ-secreting cells in response to the Cap protein of PCV2, which appeared three weeks post-vaccination and increased after challenge. By that time, no significant differences were detected on PCV2 antibody titres between vaccinated and non-vaccinated pigs, although there were significant differences on day 7 post-challenge. PCV2-inoculation induced a cellular response against the Rep protein. Such response was significantly reduced or even absent in PCV2-inoculated pigs that were previously vaccinated (V-C group), presumably as a result of a lower PCV2 replication in vaccinated animals compared to non-vaccinated ones.