Assessment of one-dose mumps-containing vaccine effectiveness on wild-type genotype F mumps viruses circulating in mainland China.

To clarify the protective effect of one-dose mumps-containing vaccines (MuCV) in mainland China, the antigenic variations of HN gene and cross-neutralization capacities between MuCV and wild type genotype F MuVs were studied. In total, 70 HN gene sequences of genotype F MuV representative strains obtained from 2001 to 2015, two types of MuCV strains, 139 pairs of pre- and post-vaccination serum samples from infants receiving one dose of MuCV vaccination were analyzed. Genotype-specific amino acid variations were observed in the potential antigenic epitopes between MuCV and wild-type genotype F MuVs circulating in mainland China. The mumps neutralization antibody titers induced by one-dose MuCV were found to be generally low. Moreover, significant differences in neutralization titers were observed between vaccine and wild-type strains. It could be concluded that one-dose MuCV had a cross-protective effect against the wild-type genotype F MuVs, but its effectiveness was limited, which might be caused by insufficient doses of MuCV vaccination and the genotype-specific antigenic differences between vaccine and wild-type MuVs as well. In addition, a poor linear correlation between mumps-specific IgG concentrations and neutralization titers was observed in this study, indicating the concentration of MuV-specific IgG could not fully reflect the neutralizing antibody titer in serum. Therefore, it is highly recommended to provide a second dose of MuCV to preschool children to increase MuV neutralizing antibody titers and use MuV cross-neutralization test as preferred tool for assessment of mumps-containing vaccine effectiveness on wild-type MuVs. This is the first report to assess the effectiveness of one-dose Chinese MuCV against wild-type genotype F MuVs, which would be benefit for the development of mumps vaccination strategy.

Influenza A virus hemagglutinin glycosylation compensates for antibody escape fitness costs.

Rapid antigenic evolution enables the persistence of seasonal influenza A and B viruses in human populations despite widespread herd immunity. Understanding viral mechanisms that enable antigenic evolution is critical for designing durable vaccines and therapeutics. Here, we utilize the primerID method of error-correcting viral population sequencing to reveal an unexpected role for hemagglutinin (HA) glycosylation in compensating for fitness defects resulting from escape from anti-HA neutralizing antibodies. Antibody-free propagation following antigenic escape rapidly selected viruses with mutations that modulated receptor binding avidity through the addition of N-linked glycans to the HA globular domain. These findings expand our understanding of the viral mechanisms that maintain fitness during antigenic evolution to include glycan addition, and highlight the immense power of high-definition virus population sequencing to reveal novel viral adaptive mechanisms.

Serological weak D phenotypes: a review and guidance for interpreting the RhD blood type using the RHD genotype.

Approximately 0·2-1% of routine RhD blood typings result in a "serological weak D phenotype." For more than 50 years, serological weak D phenotypes have been managed by policies to protect RhD-negative women of child-bearing potential from exposure to weak D antigens. Typically, blood donors with a serological weak D phenotype have been managed as RhD-positive, in contrast to transfusion recipients and pregnant women, who have been managed as RhD-negative. Most serological weak D phenotypes in Caucasians express molecularly defined weak D types 1, 2 or 3 and can be managed safely as RhD-positive, eliminating unnecessary injections of Rh immune globulin and conserving limited supplies of RhD-negative RBCs. If laboratories in the UK, Ireland and other European countries validated the use of potent anti-D reagents to result in weak D types 1, 2 and 3 typing initially as RhD-positive, such laboratory results would not require further testing. When serological weak D phenotypes are detected, laboratories should complete RhD testing by determining RHD genotypes (internally or by referral). Individuals with a serological weak D phenotype should be managed as RhD-positive or RhD-negative, according to their RHD genotype.

Assessment of immune interference, antagonism, and diversion following human immunization with biallelic blood-stage malaria viral-vectored vaccines and controlled malaria infection.

Overcoming antigenic variation is one of the major challenges in the development of an effective vaccine against Plasmodium falciparum, a causative agent of human malaria. Inclusion of multiple Ag variants in subunit vaccine candidates is one strategy that has aimed to overcome this problem for the leading blood-stage malaria vaccine targets, that is, merozoite surface protein 1 (MSP1) and apical membrane Ag 1 (AMA1). However, previous studies, utilizing malaria Ags, have concluded that inclusion of multiple allelic variants, encoding altered peptide ligands, in such a vaccine may be detrimental to both the priming and in vivo restimulation of Ag-experienced T cells. In this study, we analyze the T cell responses to two alleles of MSP1 and AMA1 induced by vaccination of malaria-naive adult volunteers with bivalent viral-vectored vaccine candidates. We show a significant bias to the 3D7/MAD20 allele compared with the Wellcome allele for the 33 kDa region of MSP1, but not for the 19 kDa fragment or the AMA1 Ag. Although this bias could be caused by "immune interference" at priming, the data do not support a significant role for "immune antagonism" during memory T cell restimulation, despite observation of the latter at a minimal epitope level in vitro. A lack of class I HLA epitopes in the Wellcome allele that are recognized by vaccinated volunteers may in fact contribute to the observed bias. We also show that controlled infection with 3D7 strain P. falciparum parasites neither boosts existing 3D7-specific T cell responses nor appears to "immune divert" cellular responses toward the Wellcome allele.

Comprehensive assessment of the TCRBV repertoire in small T-cell samples by means of an improved and convenient multiplex PCR method.

OBJECTIVE: Overall diversity of the T-cell receptor (TCR) repertoire can be regarded as a recapitulatory signature of a host's immunocompetence status. We aimed to establish a time- and cost-saving multiplex polymerase chain reaction (PCR) method for determining the TCR repertoire of conventional alphabeta T cells in small T-cell samples. MATERIALS AND METHODS: The method estimates the length distribution of the complementarity-determining regions 3 (CDR3) of beta variable (BV) gene segments (TCRBV repertoire) by multiplex PCR, followed by fluorescent run-off reactions to visualize BV-BC and/or BV-BJ rearrangements. Run-off products are separated on a capillary sequencer and subsequently analyzed with GeneScan or Genotyper programs. Detection-limit studies with normal T cells, KMS27 cells, and regulatory T cells were carried out to evaluate sensitivity and reproducibility. RESULTS: Head-to-head comparison of the method with conventional immunoscope assay has shown that it is a time- and cost-saving approach to characterize TCRBV and TCRBJ repertoires, including the presence of oligoclonal T cells in samples containing as few as 1 x 10(5) T cells. CONCLUSION: We have developed a multiplex PCR method that allows comprehensive assessment of the TCRBV repertoire at the BV-BC and BV-BJ levels, and saves a considerable amount of time, reagents, and cell input.

Long simple sequence repeats in host-adapted pathogens localize near genes encoding antigens, housekeeping genes, and pseudogenes.

Simple sequence repeats (SSRs) in DNA sequences are tandem iterations of a single nucleotide or a short oligonucleotide. SSRs are subject to slipped-strand mutations and a common source of phase variation in bacteria and antigenic variation in pathogens. Significantly long SSRs are generally rare in prokaryotic genomes, and long SSRs composed of iterations of mono-, di-, tri-, and tetranucleotides are mostly restricted to host-adapted pathogens. We present new results concerning associations between long SSRs and genes related to different cellular functions in genomes of host-adapted pathogens. We found that in the majority of the analyzed genomes, at least some of the genes associated with SSRs encode potential antigens, which is expected if the primary function of SSRs is their contribution to antigenic variation. However, we also found a number of long SSRs associated with housekeeping genes, including rRNA and tRNA genes, genes encoding ribosomal proteins, amino acyl-tRNA synthetases, chaperones, and important metabolic enzymes. Many of these genes are probably essential and it is unlikely that they are phase-variable. Few statistically significant associations between SSRs and gene functional classifications were detected, suggesting that most long SSRs are not related to a particular cellular function or process. Long SSRs in Mycobacterium leprae are mostly associated with pseudogenes and may be contributing to gene loss following the adaptation to an obligate pathogenic lifestyle. We speculate that LSSRs may have played a similar role in genome reduction of other host-adapted pathogens.

On the role of cross-immunity and vaccines on the survival of less fit flu-strains.

A pathogen's route to survival involves various mechanisms including its ability to invade (host's susceptibility) and its reproductive success within an invaded host ("infectiousness"). The immunological history of an individual often plays an important role in reducing host susceptibility or it helps the host mount a faster immunological response de facto reducing infectiousness. The cross-immunity generated by prior infections to influenza A strains from the same subtype provide a significant example. The results of this paper are based on the analytical study of a two-strain epidemic model that incorporates host isolation (during primary infection) and cross-immunity to study the role of invasion mediated cross-immunity in a population where a precursor related strain (within the same subtype, i.e. H3N2, H1N1) has already become established. An uncertainty and sensitivity analysis is carried out on the ability of the invading strain to survive for given cross-immunity levels. Our findings indicate that it is possible to support coexistence even in the case when invading strains are "unfit", that is, when the basic reproduction number of the invading strain is less than one. However, such scenarios are possible only in the presence of isolation. That is, appropriate increments in isolation rates and weak cross-immunity can facilitate the survival of less fit strains. The development of "flu" vaccines that minimally enhance herd cross-immunity levels may, by increasing genotype diversity, help facilitate the generation and survival of novel strains.

Microarray-based identification of antigenic variants of foot-and-mouth disease virus: a bioinformatics quality assessment.

BACKGROUND: The evolution of viral quasispecies can influence viral pathogenesis and the response to antiviral treatments. Mutant clouds in infected organisms represent the first stage in the genetic and antigenic diversification of RNA viruses, such as foot and mouth disease virus (FMDV), an important animal pathogen. Antigenic variants of FMDV have been classically diagnosed by immunological or RT-PCR-based methods. DNA microarrays are becoming increasingly useful for the analysis of gene expression and single nucleotide polymorphisms (SNPs). Recently, a FMDV microarray was described to detect simultaneously the seven FMDV serotypes. These results encourage the development of new oligonucleotide microarrays to probe the fine genetic and antigenic composition of FMDV for diagnosis, vaccine design, and to gain insight into the molecular epidemiology of this pathogen. RESULTS: A FMDV microarray was designed and optimized to detect SNPs at a major antigenic site of the virus. A screening of point mutants of the genomic region encoding antigenic site A of FMDV C-S8c1 was achieved. The hybridization pattern of a mutant includes specific positive and negative signals as well as crosshybridization signals, which are of different intensity depending on the thermodynamic stability of each probe-target pair. Moreover, an array bioinformatic classification method was developed to evaluate the hybridization signals. This statistical analysis shows that the procedure allows a very accurate classification per variant genome. CONCLUSION: A specific approach based on a microarray platform aimed at distinguishing point mutants within an important determinant of antigenicity and host cell tropism, namely the G-H loop of capsid protein VP1, was developed. The procedure is of general applicability as a test for specificity and discriminatory power of microarray-based diagnostic procedures using multiple oligonucleotide probes.

Current situation in the development of a preventive HIV vaccine.

The uncontrolled progression of the AIDS epidemic has made the development of an efficacious human immunodeficiency virus (HIV) vaccine a major objective of scientific research. No effective preventive vaccine against HIV is currently available and sterilizing immunity has not yet been achieved in animal models. This review analyses the major challenges in developing an AIDS vaccine, in particular the mechanisms involved in viral escape from the immune response, and summarizes the results obtained with the different prototypes of therapeutic and preventive vaccines. Finally, social, economic and healthcare aspects of research into HIV vaccines and current controversies regarding the development of clinical trials are discussed.

Quantitative assessment of sense and antisense transcripts from genes involved in antigenic variation (vsp genes) and encystation (cwp 1 gene) of Giardia lamblia clone GS/M-83-H7.

Antigenic variation of the intestinal protozoan parasite Giardia lamblia is caused by an exchange of the parasite's variant surface protein (VSP) coat. Many investigations on antigenic variation were performed with G. lamblia clone GS/M-83-H7 which produces surface antigen VSP H7. To generate novel information on giardial vsp gene transcription, vsp RNA levels were assessed by quantitative reverse transcription-(RT)-PCR in both axenic VSP H7-type trophozoites and subvariants obtained after negative selection of GS/M-83-H7 trophozoites by treatment with a cytotoxic, VSP H7-specific monoclonal antibody. Our investigation was not restricted to the assessment of the sense vsp transcript levels but also included an approach aimed at the detection of complementary antisense vsp transcripts within the two trophozoite populations. We found that sense vsp H7 RNA predominated in VSP H7-type trophozoites while sense RNA from only one (vsp IVg) of 8 subvariant vsp genes totally analysed predominated in subvariant-type trophozoites. Interestingly, the two trophozoite populations exhibited a similar relative distribution regarding the vsp H7 and vsp IVg antisense RNA molecules. An analogous sense versus antisense RNA pattern was also observed when the transcripts of gene cwp 1 (encoding cyst wall protein 1) were investigated. Here, both types of RNA molecules only appeared after cwp 1 had been induced through in vitro encystation of the parasite. These findings for the first time demonstrated that giardial antisense RNA production did not occur in a constitutive manner but was directly linked to complementary sense RNA production after activation of the respective gene systems.

Proper multivariate conditional autoregressive models for spatial data analysis.

In the past decade conditional autoregressive modelling specifications have found considerable application for the analysis of spatial data. Nearly all of this work is done in the univariate case and employs an improper specification. Our contribution here is to move to multivariate conditional autoregressive models and to provide rich, flexible classes which yield proper distributions. Our approach is to introduce spatial autoregression parameters. We first clarify what classes can be developed from the family of Mardia (1988) and contrast with recent work of Kim et al. (2000). We then present a novel parametric linear transformation which provides an extension with attractive interpretation. We propose to employ these models as specifications for second-stage spatial effects in hierarchical models. Two applications are discussed; one for the two-dimensional case modelling spatial patterns of child growth, the other for a four-dimensional situation modelling spatial variation in HLA-B allele frequencies. In each case, full Bayesian inference is carried out using Markov chain Monte Carlo simulation.

Malaria multigene families: the price of chronicity.

In this article, Georges Snounou, William Jarra and Peter Preiser discuss the survival strategy of malaria parasites in the light of a novel mechanism of clonal phenotypic variation recently described for a multigene family of Plasmodium yoelii yoelii. The 235 kDa rhoptry proteins (Py235) encoded by these genes may be involved in the selection of red blood cells for invasion by merozoites. The new mechanism may explain the ability of individual parasites to adapt to natural variations in red blood cell subsets, while ensuring that sufficient merozoites escape immune attack, thus maintaining a chronic infection for extended periods. This counterpoints the antigenic variation exemplified by PfEMP1 proteins (a large family of proteins derived from P. falciparum), which operates at the population level. The possibility of manipulating the expression of functionally similar genes in other Plasmodium species could lead to therapies aimed at reducing clinical severity without compromising the acquisition and maintenance of immunity.