Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “synonymous variant”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 487 records · Page 27Linked to original sources

Liposarcoma: new entities and evolving concepts.

Liposarcoma is the most common soft tissue sarcoma and accounts for approximately 20% of all mesenchymal malignancies. In the last decade, the results of several studies have led to the delineation of new variants as well as to the introduction of new concepts, mainly as a result of the fruitful interactions between genetics and pathology. Spindle cell liposarcoma represents an uncommon variant of well-differentiated liposarcoma. It tends to occur in adults and often involves the subcutaneous soft tissue. However, from the observation of a larger number of cases, the anatomic distribution of spindle cell liposarcoma seems to be comparable to that of the other well-differentiated liposarcoma subtypes. Spindle cell liposarcoma tends to recur locally and may dedifferentiate. Morphologically it is composed of a fairly bland neural-like spindle cell proliferation set in a fibrous and/or myxoid background and is associated with an atypical lipomatous component. Great debate has been generated by the introduction of the term atypical lipoma to emphasize the fact that well-differentiated liposarcoma shows risk of local recurrence but no potential for metastasis. In our opinion well-differentiated liposarcoma and atypical lipoma should be considered synonyms that describe lesions identical both morphologically and kayotypically. Dedifferentiated liposarcoma is a distinct type of liposarcoma in which transition from low-grade to high-grade nonlipogenic morphology within a well-differentiated liposarcoma is observed. The transition usually occurs in an abrupt fashion; however, in rare cases it can be more gradual. Recently, it also has been proposed that dedifferentiated liposarcoma should be further classified into low and high grade. Dedifferentiated liposarcoma rarely exhibits heterologous (most often myoid) differentiation. A peculiar "neural-like whorling pattern" of dedifferentiation also has been described recently. Surprisingly, the clinical outcome of dedifferentiated liposarcoma is less aggressive that in other high-grade pleomorphic sarcomas but genetic as well as molecular data exist that may partiallyjustify such a discrepancy. Myxoid and round cell liposarcoma, even if still classified by the World Health Organization as two distinct subtypes, share both clinical and morphologic features. Lesions combining both patterns are very frequent and wide agreement exists in considering round cell liposarcoma as the high-grade counterpart of myxoid liposarcoma. Furthermore, myxoid and round cell liposarcoma share the same characteristic chromosome change. Albeit rare, it has been recently shown that liposarcoma indeed can occur as a primary skin lesion. It often presents clinically as a dome-shaped or polypoid lesion that, histologically, most frequently shows high-grade morphologic features but carries a comparatively good prognosis. Considering currently available data, the most logical classification of liposarcoma is into three main groups: (1) well-differentiated liposarcoma (including adipocytic, sclerosing, inflammatory, spindle-cell, and dedifferentiated variants), characterized by ring or long markers chromosomes derived from the long arm of chromosome 12; (2) myxoid and round cell (poorly differentiated myxoid) liposarcoma, characterized in most cases by a reciprocal translocation t(12;16)(q13;p11); and (3) pleomorphic liposarcoma, characterized by complex karyotypes.

Adult↗

HVR-1 quasispecies modifications occur early and are correlated to initial but not sustained response in HCV-infected patients treated with pegylated- or standard-interferon and ribavirin.

BACKGROUND/AIMS: HVR-1 quasispecies composition and evolution were investigated in patients chronically infected with genotype 1b HCV, treated with PEG-IFN alpha 2b or STD-IFN alpha 2b plus RBV. METHODS: HVR-1 heterogeneity was assessed by calculating nucleotidic complexity, diversity, synonymous (S) and non-synonymous (NS) substitutions at baseline, after 4 weeks of therapy (T1) and at follow-up (T18). Evolution of viral quasispecies was analysed by constructing phylogenetic trees. RESULTS: No correlation of baseline viremia with heterogeneity was observed. Nucleotidic complexity was lower in patients showing early virological response, and tended to be inversely correlated to viral load decline at 4 weeks of treatment. In the majority of SR, profound changes of quasispecies composition occurred during 4 weeks of treatment, while in NR virtually no major changes of pre-therapy variants were observed. Relapse showed both patterns of quasispecies evolution. Virus quasispecies after follow-up was similar to that found at T1 in both Relapsers and NR patients. CONCLUSIONS: Baseline parameters of HVR-1 heterogeneity seem to be involved in the early response to treatment, and early response is associated with profound variations in the HVR-1 quasispecies. Viral quasispecies surviving early therapeutic pressure are most likely able to give rise to either virus rebound or persistence at T18.

Adult↗

Immune surveillance against virus-induced tumors and nonrejectability of spontaneous tumors: contrasting consequences of host versus tumor evolution.

Spontaneous tumours are defined as tumors that develop in the absence of all experimental interference. In contrast to the widely documented, strong rejection reactions against most virus-induced tumors, spontaneous tumors evoke little or no detectable rejection reaction in intact or preimmunized syngeneic hosts. The difference can be viewed in relation to the contrasting natural history of the two conditions. Spontaneous tumors evolve in several steps, as a fule. "Tumor progression" is a microevolutionary process at the level of the somatic tissue where successive clonal variants replace each other. Each new variant gains the upper hand due to its greater independence of some restricting host mechanism. Independence of immune restrictions must be part of this process. Host selection for immune resistance apparently plays no major role here, presumably because most of the naturally occurring tumors arise after the host has passed the peak of its reproductive period. Protection against the oncogenic effects of ubiquitous tumor viruses is, on the other hand, the result of host selection for immune mechanisms favoring prompt rejection of virus-transformed cells. This is neither synonymous with nor related to protection against the viral infection per se, which is frequently successful and usually quite harmless. A certain relationship can be perceived between the degree of viral ubiquity and the strength of immune protection against the corresponding tumor cells. Natural selection for host recognition of commonly occurring, virally induced changes in neoplastic cell membranes can be surmised to occur, at least in part, by the fixation of appropriate immune responsiveness (Ir) genes. The role of Ir genes for tumor recognition can be approached by the genetic analysis of the F1 hybrid resistance effect. Unresponsiveness to spontaneous tumors may be overcome by target-cell modification, e.g., by chemical coupling, somatic cell hybridization, or viral "xenogenization".

Animals↗

Relationships between genomic base content and distribution of mass in coded proteins.

The aim of this research was to examine the possible significance of genome/protein relationships in terms of effects on distribution of mass, especially in proteins. Amino acid residues in proteins have side-chains and polypeptide segments. We use "SCM" (side-chain mass), "MCM" (main-chain mass), and "deltaM" (SCM-MCM) as the deviation from "mass balance." Total MCM of the 61 amino acids in the standard code, 3412, equals total SCM: they form a mass balanced set (mean deltaM = 0). Of 14 natural variants of the code, seven have slightly positive mean deltaM values and seven have slightly negative values. Codes with the standard amino acids assigned randomly to the 20 codon sets of the standard code have about one chance in 3,300 of producing a mass balanced set. In natural proteins, as %A + T increases, the proportion of the mass in the side-chains also increases, by about half the amount calculated for standard genes with various AT/GC ratios, partly due to selection of codons with greater variability in composition at synonymous sites. For 203 representative species (including organelles), the total protein mass is distributed approximately equally between SCM and MCM (overall mean deltaM/amino acid residue, -0.06). The attainment of some overall macromolecular mass balance may have been a criterion for selecting the codon/amino acid pairs. When both structural and dynamic requirements are considered, a genetic code based on hydrophobicity and mass balance as key properties seems likely.

AT Rich Sequence↗

Allelic variants of the human MHC class I chain-related B gene (MICB).

The human major histocompatibility complex (MHC) is located within a 4 megabase segment on chromosome 6p21.3. Recently, a highly divergent MHC class I chain-related gene family, MIC was identified within the class I region. The MICA and MICB genes in this family have unique patterns of tissue expression. The MICA gene is highly polymorphic, with more than 20 alleles identified to date. To elucidate the extent of MICB allelic variations, we sequenced exons 2 (alpha 1), 3 (alpha 2), 4 (alpha 3), and 5 (transmembrane) as well as introns 2 and 4 of this gene in 46 HLA homozygous B-cell lines. We report the identification of eleven alleles based on seven non-synonymous, two synonymous, and four intronic nucleotide variations. Interestingly, one allele has a nonsense mutation resulting in a premature termination codon in the alpha 2 domain. Thus, MICB appears to have fewer alleles than MICA, not unlike the allelic ratio between the HLA-C and -B loci. A preliminary linkage analysis of the MICB alleles with those of the closely located MICA and HLA-B genes revealed no conspicuous linkage disequilibrium between them, implying the presence of a potential recombination hotspot between the MICB and MICA genes.

Alleles↗

Identification of the gene variations in human CD22.

CD22, a member of the immunoglobulin superfamily, is a B-cell transmembrane glycoprotein that acts as an accessory-signaling component of the B-cell antigen receptor (BCR). Recent evidence indicating the role of CD22 as a negative regulator of BCR signal transduction prompted us to test the possibility that genetic variations of human CD22 may be associated with autoimmune diseases. In this study, variation screening of the entire CD22 coding region was performed, and possible association with rheumatic diseases was tested, using the genomic DNA from 207 healthy Japanese individuals, 68 patients with systemic lupus erythematosus (SLE), and 119 patients with rheumatoid arthritis (RA). Through the variation screening, seven non-synonymous and four synonymous substitutions were identified. In addition, single base substitutions were found in two introns flanking exon-intron junctions. Among these variations, Q152E substitution within the second extracellular domain was observed with a marginally higher frequency in the patients with SLE (3/68, 4.4%) than that in healthy individuals (1/207, 0.5%) (P=0.048. SLE vs healthy individuals), although this difference was no longer significant after correction for the number of comparisons (Pc=0.62). No significant association was observed between any of the variations and RA. These findings indicate that a number of genetic variants are present in CD22, and suggest that CD22 could be considered a candidate for the susceptibility genes to autoimmune diseases.

Adolescent↗

The success of therapeutic communities for substance abusers in American prisons.

Residential treatment provides opportunities for intensive interventions and support that may not be present in outpatient settings. In the area of substance abuse treatment, the therapeutic community (TC) has become synonymous with residential treatment. A growing body of prison TC outcome research has led to recent acceptance of prison TCs as a major innovation in American correctional institutions. An overview of prison TC outcome research is provided and the emergence of the TC as the primary substance abuse treatment modality in prison is described. The self-help orientation that provides the basis for both residential and 12-Step substance abuse treatment programs is described and contrasted with the relapse recovery model. The theoretical principles of the TC model are discussed and two main variants of the prison TC model are described and contrasted. Finally, recommendations are offered for expanding the TC approach and increasing its effectiveness by treating comorbid problems that are prevalent among prison inmates with substance abuse problems.

Humans↗

Human phenylethanolamine N-methyltransferase pharmacogenomics: gene re-sequencing and functional genomics.

Phenylethanolamine N-methyltransferase (PNMT, EC2.1.1.28) catalyzes the N-methylation of norepinephrine to form epinephrine. As a step toward understanding the possible contribution of inheritance to individual variation in PNMT-catalyzed epinephrine formation, we 're-sequenced' the entire human PNMT gene, including the three exons, the introns and approximately 1 kb of the 5'-flanking region (5'-FR), using DNA samples from 60 African-American (AA) and 60 Caucasian-American (CA) subjects. Within the 3.5 kb re-sequenced, 18 single nucleotide polymorphisms (SNPs) were observed, including four non-synonymous coding SNPs (cSNPs) that resulted in the following alterations in encoded amino acid sequence: Asn9Ser, Thr98Ala, Arg112Cys and Ala175Thr. When constructs for the non-synonymous cSNPs were transiently expressed in COS-1 cells, the Ala98 allozyme displayed significantly lower levels of both activity and immunoreactive protein (p < 0.002) than did the wild-type (WT) enzyme due, at least in part, to accelerated protein degradation by a proteasome-mediated process. Luciferase reporter gene constructs were also created for the six common PNMT 5'-FR haplotypes observed. Significant differences were observed among haplotypes in their ability to drive transcription. These observations raise the possibility of inherited variation in the ability to form epinephrine from norepinephrine as a result of variant PNMT polymorphisms and haplotypes.

Animals↗

Association of Fcgamma receptor IIB gene polymorphism with genetic susceptibility to systemic lupus erythematosus in Chinese populations--a family-based association study.

BACKGROUND: The aim of this study was to investigate the role of FcgammaRIIB gene in susceptibility to systemic lupus erythematosus (SLE) using family-based association analysis method, and to examine possible haplotypes between two single-nucleotide polymorphisms. OBJECTIVE: A total of 119 patients with SLE from 95 nuclear families, aged from 14 to 78 years, was selected according to 1997 criteria of American College of Rheumatology (ACR), In addition, 316 family members of these patients were also genotyped. METHODS: A family-based association study was used to explore the relationship between gene polymorphism and SLE. We studied two single-nucleotide polymorphisms (SNPs) encoding non-synonymous substitution in the FcgammaRIIB gene with respect to genetic susceptibility to SLE. The FcgammaRIIB gene was genotyped by restriction fragment length polymorphism (RFLP) method. RESULTS: Among 119 SLE patients, the frequencies of FcgammaRIIB-C50T CC, CT and TT genotypes were 12.7%, 60.7% and 26.6%, respectively. The frequencies of FcgammaRIIB-T225C TT, TC and CC genotypes were 8.1%, 61.3% and 30.6%, respectively. Four haplotypes, 50T-225C (34.1%), 50C-225C (27.7%), 50T-225T (19.7%) and 50C-50T (18.5%) were reconstructed. Univariate (single-marker) family-based association tests (FBATs) demonstrated that variant alleles at two SNPs, rs10917661 and rs1050501, in exons 2 and 5 of FcgammaRIIB gene were significantly associated with genetic susceptibility to SLE in additive model (exon 2, Z=3.444, P=0.00057; exon 5, Z=3.707, P=0.00020), respectively. Transmission/disequilibrium test (TDT) and sibship disequilibuium test (SDT) analysis showed an excess of the alleles of T (C50T) and C (T225/C) from heterozygous parents to affected offspring (chi(2)=10.88, P=0.0013; chi(2)=7.14, P=0.0105, respectively). Furthermore, the haplotype-specific FBATs showed 50T-225C (34.1%) haplotype was more frequently transmitted in SLE than other haplotypes (Z=3.539, P=0.00042). CONCLUSIONS: Our findings provide strong evidence suggesting the FcgammaRIIB-50T-225C haplotype might be the susceptible factor of SLE in Chinese population.

Adolescent↗

Lichen myxedematosus (papular mucinosis): new concepts and perspectives for an old disease.

Lichen myxedematosus (LM) is an idiopathic cutaneous mucinosis; its classification dates back to 1953, when Montgomery and Underwood distinguished 4 types of LM. In the literature, the terms LM, papular mucinosis, and scleromyxedema often have been used indiscriminately as synonyms, but most reported cases of LM or papular mucinosis without indication of the subtype appear in fact to be cases of scleromyxedema. Actually, LM includes 2 clinicopathologic subsets: a generalized papular and sclerodermoid form (the only one which should be called scleromyxedema) with systemic, even lethal, manifestations and a localized form, which does not run a disabling course. The localized form is subdivided into 4 subtypes: (1) a discrete papular form involving any site; (2) acral persistent papular mucinosis involving only the extensor surface of the hands and wrists; (3) papular mucinosis of infancy, a pediatric variant of the discrete form or the acral form of persistent papular mucinosis; and (4) nodular form. A third group of atypical or intermediate forms, not meeting the criteria for either scleromyxedema or the localized form, includes cases of (1) scleromyxedema without monoclonal gammopathy, (2) localized forms with monoclonal gammopathy and/or systemic symptoms, (3) localized forms with mixed features of the subtypes, and (4) not well-specified cases.

Humans↗

Combinatorial saturation mutagenesis by in vivo overlap extension for the engineering of fungal laccases.

Combinatorial saturation mutagenesis -CSM- is a valuable tool for improving enzymatic properties from hot-spot residues discovered by directed enzyme evolution or performing semi-rational studies. CSM coupled to a reliable high-throughput screening assay -coefficient of variance below 10%- has been used to enhance turnover rates in the fungal laccase variant T2 from Myceliophthora thermophila. The influence of the highly conserved pentapeptide 509-513 on the redox potential of blue-copper containing enzymes is well described. We focused combinatorial saturation mutagenesis in residues Ser510 and Leu513. Libraries were constructed in Saccharomyces cerevisiae by in vivo overlap extension -IVOE- of the PCR products. This methodology provides a simple manner to build CSM libraries avoiding extra PCR reactions, by-products formation and in vitro ligation steps. After exploring more than 1,700 clones, mutant (7E1) with approximately 3-fold higher kinetics than parent type was found. 7E1 showed one synonymous mutation (L513L, CGT/TTG) and one beneficial mutation S510G (TCG/GGG) that can not be achieved by conventional error-prone PCR techniques. Mutation S510G seems to affect the C-terminal plug, which modulates the transit of water and oxygen to the trinuclear copper cluster.

Ascomycota↗

Well-differentiated liposarcoma (atypical lipomatous tumors).

Well-differentiated (WD) liposarcoma accounts for about 40% to 45% of all liposarcomas therefore representing the larger subgroup of adipocytic malignancies. It tends to occur equally in the retroperitoneum or the limbs followed by the paratesticular area and the mediastinum, with a peak incidence between the fifth and the seventh decades. WD liposarcoma is further subdivided in the adipocytic (lipoma-like), sclerosing, inflammatory, and spindle cell subtypes, of which the first two are by far the commoner. WD adipocytic liposarcoma is composed of a relatively mature adipocytic proliferation, featuring cell size variation as well as at least focal nuclear atypia. A varying number (from many to none) of lipoblasts may be found. Sclerosing WD liposarcoma is characterized microscopically by the presence of scattered distinctive bizarre stromal cells and multivacuolated lipoblasts set in a fibrillary collagenous background. Inflammatory liposarcoma represents a rare variant of WD liposarcoma in which a chronic inflammatory infiltrate predominates to the extent that the differential diagnosis is mainly with nonadipocytic lesions such as inflammatory myofibroblastic tumor, Castleman's disease, and Hodgkin's as well as non-Hodgkin's lymphomas. Spindle cell liposarcoma is the rarest variant and is composed neural-like spindle cell proliferation set in a fibrous and/or myxoid background and associated with an atypical lipomatous component which usually includes lipoblasts. Cytogenetically, WD liposarcoma appears to be relatively homogenous exhibiting characteristic ring as well as giant marker chromosomes containing amplified genetic material derived from the 12q13-15 chromosome region. As WD liposarcomas of any type have no potential for metastasis unless they undergo dedifferentiation, the opportunity to replace the term "WD liposarcoma" with a less frightening denomination has produced a long, sharp debate. WD liposarcoma and atypical lipoma should be considered as synonyms and their use should therefore be determined by the degree of reciprocal comprehension between the surgeon and the pathologist to prevent either inadequate or excessive treatment.

Adipocytes↗

Polymorphisms of CD36 in Thai malaria patients.

The human protein CD36 is a major endothelial receptor for Plasmodium falciparum parasitized erythrocytes. Several polymorphisms causing CD36 deficiency have been identified to date: T1264G in Kenyan and Gambian patients, and C478T, 539delAC, and 1159insA in Japanese patients. The T1264G polymorphism is reportedly associated with protection from severe malaria in Kenyans, although there is a contradictory report suggesting the susceptibility of T1264G to severe malaria. The polymorphism of CD36 has not been thoroughly studied in Asian malaria patients. In this study, nucleotide sequence variations in exons 4, 5, 6, and 10 of CD36 were investigated in mild and cerebral malaria patients living in northwest Thailand. A novel synonymous substitution T1168C was detected in exon 10, whereas no variation was found in exons 4 and 6. The 539delAC allele in exon 5 was detected in Thai malaria patients, while T1264G, C478T, and 1159insA were not found. The 539delAC allele was observed in three cerebral malaria patients (3/107), but not in mild malaria patients (0/203). The frequency of 539delAC was significantly higher in cerebral malaria patients than in mild malaria patients (p = 0.040, Fisher's exact test). Although independent studies should be performed in order to confirm our findings, the 539delAC allele might be a high-risk variant for cerebral malaria in Thai.

Adult↗

Genotypic and phenotypic correlates of the HIV Type 1 env gene evolution in infected children with discordant response to antiretroviral therapy.

The genotypic-phenotypic correlates of human immunodeficiency virus type 1 (HIV-1) env gene evolution were investigated in samples from eight infected children under antiretroviral therapy (ART) and virological failure. Evolution of the gp120 C2-V5 env sequence was demonstrated in all subjects but one by sequence analysis of the replicating plasma virus collected at baseline and 12-15 months after ART initiation. The analysis of the host's selective pressure showed that in four subjects, the ratio of nonsynonymous to synonymous amino acid substitutions was higher in the V3 sequences than in the C2-V5 region ([K (a)/K (s)](V3)/[K (a)/K (s)](C2V5) >1.0). Interestingly, this feature was observed only in subjects (four of five) showing an increase in T cell receptor rearrangement excision circle (TREC)-bearing cells and in CD4(+) T-lymphocytes despite persistent viremia (discordant therapeutic response) (p = 0.02), thus suggesting that the V3 loop is a target of the immune reconstitution under ART. Using phenotypic analysis of recombinant viruses expressing exogenous V3 sequences, a reverse shift from CXCR4-tropic to CCR5-tropic variants was demonstrated in two of the four subjects, further indicating that the host's selective pressure sharply forces the V3 evolution of replicating variants. The data indicate that a complex HIV-1-host interplay occurs in children receiving antiretroviral treatments and suggest that the recovery of thymic function places a selective constraint on the viral V3 loop.

Anti-Retroviral Agents↗

Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing.

Studies of expressed sequence tag data sets have revealed large numbers of splicing variants for human genes, but it remains challenging to distinguish functionally important variants from aberrant splicing, clarify the nature of the alternative functions, and understand the signals that regulate splicing choices. To help address these issues, we have constructed and analyzed a large data set of 1,478 exon-skipping alternative splicing (AS) variants evolutionarily conserved in human and mouse. In about one-fifth of cases, one isoform appears subject to nonsense-mediated mRNA decay (NMD), supporting the idea that a major role of AS is to regulate gene expression; one-quarter of these NMD-inducing cases involve a conserved exon whose apparent sole purpose is to mediate destruction of the message when included. We explore sequence conservation likely related to splicing regulation, using in part a measure of the overall amount of conserved information in a sequence, and find that the increased conservation that has been observed within AS exons primarily affects synonymous sites, suggesting that regulatory signals significantly constrain synonymous substitution rates. We show that a lower frequency of the inclusion isoform relative to the exclusion isoform tends to be associated with weaker splice site signals, smaller exon size, and higher intronic sequence conservation, and provide evidence that all of these factors are under selection to control relative isoform frequencies. Some conserved instances of AS appear to represent aberrant splicing events that by chance have occurred in both species, and we develop a nonparametric likelihood approach to identify these.

Alternative Splicing↗

Immune avoidance strategies in RNA viruses: fitness continuums arising from trade-offs between immunogenicity and antigenic variability.

Highly exposed and protruding amino acid sites on the surface of viral capsids are subject to fewer residue interactions and packing constraints than those buried within protein interiors. Consequently they often experience higher rates of non-synonymous substitution and exhibit greater genetic variability than buried interior sites. However such protrusive surface structures often induce host immune responses and are likely to constitute B cell epitopes. Genetic variation at these surface sites is therefore likely to correspond to antigenic variation. This may be of adaptive value to the virus for two quite different reasons. The first is that antigenic variation arising over the course of a viraemia may result in greater net viral replication, and increased opportunities for viral transmission. The second is that antigenic variation generated rapidly over a single infection or incrementally over several sequential infections may give rise to variants that are sufficiently immunologically distinct that they can reinfect host individuals with previous infection experience of related virus. This would lead to an extension of the susceptible host pool with consequent increase in transmission opportunities. The surface architecture of viral capsid proteins is therefore conceivably subject to two opposing selection pressures: one to minimize the surface area accessible to interaction with elements of the immune system, the other to increase the potential access to antigenic variation by adoption of exposed and unconstrained protein conformations. Therefore, there exists a possible trade-off between the fitness benefits deriving from potential ability to generate antigenic variation, and the increased immunogenicity with which such potential may be associated. We propose that the existence of this trade-off would lead to a continuum of different strategies by which a virus might combat an immune response. We explore this strategy space with simple mathematical models, and show that peak loads of infectious virus particles are proportional to levels of antigenic diversity, and inversely proportional to immunogenicity, thereby creating the potential for a trade-off by which fitness might be maintained with a continuum of strategies. This may remain possible even if the antigenic variants are not transmissible between hosts, so long as immune resources are sufficiently dispersed between antigenic variants. The diversity of possible strategies is discussed with reference to the Picornavirus family.

Antibodies, Viral↗

Evidence for positive selection in foot-and-mouth disease virus capsid genes from field isolates.

The nature of selection on capsid genes of foot-and-mouth disease virus (FMDV) was characterized by examining the ratio of nonsynonymous to synonymous substitutions in 11 data sets of sequences obtained from six different serotypes of FMDV. Using a method of analysis that assigns each codon position to one of a number of estimated values of nonsynonymous to synonymous ratio, significant evidence of positive selection was identified in 5 data sets, operating at 1-7% of codon positions. Evidence of positive selection was identified in complete capsid sequences of serotypes A and C and in VP1 sequences of serotypes SAT 1 and 2. Sequences of serotype SAT-2 recovered from a persistently infected African buffalo also revealed evidence for positive selection. Locations of codons under positive selection coincide closely with those of antigenic sites previously identified with the use of monoclonal antibody escape mutants. The vast majority of codons are under mild to strong purifying selection. However, these results suggest that arising antigenic variants benefit from a selective advantage in their interaction with the immune system, either during the course of an infection or in transmission to individuals with previous exposure to antigen. Analysis of amino acid usage at sites under positive selection indicates that this selective advantage can be conferred by amino acid substitutions that share physicochemically similar properties.

Amino Acid Sequence↗