Detection and complete genome sequence of a divergent isolate of cucumber fruit mottle mosaic virus on Coccinia grandis in Sudan.

Cucurbit-infecting tobamoviruses known so far belong to six acknowledged or tentative species. Except for cucumber green mottle mosaic virus (CGMMV), which is present worldwide, they are geographically restricted, mostly to Asia, and have not been observed in Africa so far. A tobamovirus isolate infecting a wild Coccinia grandis plant was collected in central Sudan in 2012. Its host range appeared to be mostly limited to cucurbits. Its full-length genome sequence was determined and found to be 85% identical to those of isolates of cucumber fruit mottle mosaic virus (CFMMV) described in Israel and Korea, whereas the aa sequence identity to CFMMV isolates was 92 to 95%, depending on the protein. Based on its biological and molecular properties, we suggest that the Sudanese isolate should be considered a divergent isolate of CFMMV. This is the first description of CFMMV in Africa. Its high divergence from isolates from Israel and Korea suggests a lack of recent exchanges between CFMMV from Sudan and the other known populations.

Characterization and occurrence of squash chlorotic leaf spot virus, a tentative new torradovirus infecting cucurbits in Sudan.

During a survey conducted in Sudan in 2012, a virus with spherical particles was isolated from a squash plant showing chlorotic leaf spots. The virus was transmitted mechanically and by two whitefly species, but not by aphids. RT-PCR with generic torradovirus primers yielded a band of expected size from total RNA of a symptomatic plant. Next-generation sequencing confirmed that this is tentatively a new torradovirus, for which we propose the name 'squash chlorotic leaf spot virus'. Using specific RT-PCR primers, the virus was detected in cucurbit samples collected since 1992 at different locations in Sudan.

New species in the papaya ringspot virus cluster: Insights into the evolution of the PRSV lineage.

The "Papaya ringspot virus (PRSV) cluster" of cucurbit-infecting potyviruses contains five acknowledged species that have similar biological, serological and molecular properties. Additional data suggest there are other uncharacterized species from various locations in the world that likely belong to the PRSV cluster including a new PRSV-like virus reported from Sudan in 2003. Molecular and biological data indicated that the virus from Sudan belongs to a new species, tentatively named wild melon vein banding virus (WMVBV). The complete nucleotide sequence of a second virus from Sudan revealed it was a divergent relative of Moroccan watermelon mosaic virus (MWMV). Based on sequence similarity this virus was determined to be a distinct species and tentatively named Sudan watermelon mosaic virus (SuWMV). Molecular analyses indicate that SuWMV is a recombinant between WMVBV- and MWMV-related viruses. Based on surveys performed in Sudan between 1992 and 2012, SuWMV appeared 10 times more frequent than WMVBV in that country (14.6% vs. 1.5% of the samples tested). The geographic structure and molecular diversity patterns of the putative and acknowledged species suggest that the PRSV-like cluster originated in the Old World about 3600 years ago, with an important diversification in Africa.

Evaluation of an expert system linked to a rapid antibiotic susceptibility testing system for the detection of beta-lactam resistance phenotypes.

Interpretive reading of antibiotic disc agar diffusion tests indicates the resistance mechanisms, if any, expressed by a bacterium. An expert system for determining resistance mechanisms using rapid automated antibiotic susceptibility tests has been developed. The beta-lactam susceptibility of each of 300 strains of clinically significant species of enterobacteria, displaying natural and acquired resistance mechanisms, was determined by disc agar diffusion and by a rapid automated method of susceptibility testing associated with an expert system. For every strain, the conclusion of the expert analysis of the automated test was compared with the commonly accepted interpretation of disc agar diffusion tests. Of the 300 strains studied, 275 were similarly interpreted (91.7% agreement). The susceptible and naturally beta-lactam-resistant phenotypes (wild phenotypes) were equally recognized by both methods. Similarly, the results of the two methods concurred for most of the acquired resistance phenotypes. However, for 25 strains (8.3%) the results diverged. The expert system proposed an erroneous phenotype (5 strains), several phenotypes including the correct one (17 strains), or no phenotype (1 strain). For 2 strains the natural resistance mechanism was not detected at first by the automated method but was subsequently deduced by the expert analysis according to bacterial identification. These results demonstrate that satisfactory interpretive reading of automated antibiotic susceptibility tests is possible in 4 to 5 hours but requires careful selection of the antibiotics tested as phenotypic markers.

[Limy bile syndrome. Study of a case with double localization in the gallbladder and common bile duct]. / Le syndrome de la bile calcique. Etude d'un cas à double localisation vésiculaire et cholédocienne.

We report the case of a patient with limy bile located in both the gallbladder and common bile duct, and disappearing spontaneously. Since the first description of this syndrome in 1911, approximately 300 cases have been reported in the literature, including 20 cases with double localization. The male/female ratio was 1/3. All patients were more than 40 year old. Conventional radiogram was sufficient to establish diagnosis. Spontaneous disappearance of limy bile is rare. The etiopathogenesis remains unclear; cholecystectomy is appropriate.

Comparative molecular epidemiology provides new insights into Zucchini yellow mosaic virus occurrence in France.

Zucchini yellow mosaic virus (ZYMV, genus Potyvirus) causes important crop losses in cucurbits worldwide. In France, ZYMV epidemics are sporadic but occasionally very severe. This contrasts with Watermelon mosaic virus (WMV, genus Potyvirus) which causes regular and early epidemics. Factors influencing ZYMV epidemiology are still poorly understood. In order to gain new insights on the ecology and epidemiology of this virus, a 5-year multilocation trial was conducted in which ZYMV spread and populations were studied in each of the 20 plot/year combinations and compared with WMV. Search for ZYMV alternative hosts was conducted by testing weeds growing naturally around one plot and also by checking ZYMV natural infections in selected ornamental species. Although similar ZYMV populations were observed occasionally in the same plot in two successive years suggesting the occurrence of overwintering hosts nearby, only two Lamium amplexicaule plants were found to be infected by ZYMV of 3459 weed samples that were tested. The scarcity of ZYMV reservoirs contrasts with the frequent detection of WMV in the same samples. Since ZYMV and WMV have many aphid vectors in common and are transmitted with similar efficiencies, the differences observed in ZYMV and WMV reservoir abundances could be a major explanatory factor for the differences observed in the typology of ZYMV and WMV epidemics in France. Other potential ZYMV alternative hosts have been identified in ornamental species including begonia. Although possible in a few cases, exchanges of populations between different plots located from 500 m to 4 km apart seem uncommon. Therefore, the potential dissemination range of ZYMV by its aphid vectors seems to be rather limited in a fragmented landscape.

Bent-limb disease in lambs. Apparent transmission with an autosomal recessive gene linked to the OL-Z minor lymphocyte antigen locus and the I locus involved in the expression of R and O antigens in sheep.

In crossbred Charmois lambs, Bent-limb disease appears to be associated with the phenotype 'z,i' which corresponds to a doubly recessive genotype at the two loci OL-Z (a minor lymphocyte antigen locus independent of OLA, the major histocompatibility complex of the sheep) and I (involved in genetic control of the expression of R and O antigens found in various body fluids and on erythrocytes). The disease seems to be controlled by a single autosomal recessive gene, provisionally named bl (its normal or healthy allele Bl being dominant) which is distinct from, though linked to, the genes at the OL-Z and I loci (observed haplotype: bl,z,i). In the Lacaune breed, besides the already observed bl,z,i haplotype, there is an additional one: bl,z,I. In Vendéen sheep, and in animals which belong to two other breeds, the bl,Z11,I haplotype (bl linked to the two dominant alleles) appears to be relatively frequent. Further studies are needed in order to confirm the genetic hypothesis suggested by the present data.

Sheep major histocompatibility (OLA) complex: apparent involvement in a flock endemic infection by Corynebacterium pseudotuberculosis.

In a Préalpe flock with endemic infection by Corynebacterium pseudotuberculosis, some sires seem to have transmitted some resistance traits not yet genetically defined. In sire progenies including offspring with and without abscess, abscesses occurred independently of the transmitted sire's OLA haplotype. However, in all considered offspring, some OLA antigens were positively or negatively associated with the delayed occurrence of abscess. The three antigens OLA-A4, A10, B6 were positively associated with delayed abscess and negatively with early abscess. Conversely, antigen OLA-A2 was negatively associated with delayed abscess and to a less extent positively with early abscess. When the three following groups of offspring without abscess (a), with late abscess (b) and with early abscess (c) were compared, frequencies of genes OLA-A4, A10, B6 on the one hand, OLA-A2 on the other hand, varied inversely, which shows that the OLA complex is linked to, at least, one locus from which the genes are implied in the delay of abscess formation (or precocity). Similarly, antigen OL-X5, loosely linked with the OLA complex, appeared to be positively associated with recurrent abscess and negatively with unique abscess. The observed associations were probably caused by linkage disequilibria between OLA (and OL) genes and genes influencing either the abscess delay or recurrence.

[The sheep OL lymphocyte antigen system: 11 factors detected by microcytotoxicity assays in a prealp flock]. / Le système d'antigènes lymphocytaires OL du mouton. Etude, dans un troupeau de race préalpe, de onze facteurs décelés par microcytotoxicité

By means of microcytotoxicity techniques and using 9 immune allosera, 11 lymphocyte factors were determined in Prealpe sheep, 10 factors, transmitted by haplotypes, depended genetically on 2 linked locus: OL-A and OL-B. From a sample of 130 haplotypes, 36 OL-A alleles were demonstrated by 6 combinations of 1 to 2 factors and 80 OL-B alleles by 32 combinations of 1 to 5 factors. Genic frequencies were varied and low: inferior to 0,01 for half of the combinations they only once exceeded 0,1. The overall frequency of marked genes was estimated to 0,27 for OL-A and 0,61 for OL-B. The genetic transmission of the 11th factor (frequency: 0,05) depended on a 3rd OL-C locus of the same system.

[The major OLA histocompatibility complex in sheep. Study of 6 new factors and definition of a 3rd locus of the complex: OLA-C]. / Le complexe majeur d'histocompatibilité OLA du Mouton. Etude de six nouveaux facteurs et définition d'un troisième locus du complexe: OLA-C.

6 new OLA factors of the Sheep histocompatibility complex are described. 3 of them, C 14, C 15, C 17 are the products of 3 alleles at a third locus of the complex: OLA-C, closely linked to OLA-A and B. Two factors A 13 and B 12 are the products of 2 alleles at OLA-A and B loci. The last factor (16) is the product of an OLA gene, the locus of which is not yet defined. 28 haplotypes are described. Genes at the 3 OLA loci are in linkage disequilibrium.

Comparison of the segregation of sheep histocompatibility genes OLA - A1, A8, B7, B9, and OLX-5 in eighteen hamster X sheep fibroblast hybrid lines.

Four OLA factors of the ovine histocompatibility complex and the OLX -5 factor were recognized in hamster cell X sheep fibroblast hybrids, by means of absorption of OLA reagents with hybrid cells. Segregation of these factors could be studied in eighteen independent hybrids. In the case described, the four OLA factors were distributed into two haplotypes isolated in some hybrids. The heterozygous OLX-5 factor was linked to only one haplotype; nevertheless a dissociation, occurred in one hybrid (relative to five simultaneous transmissions), is in agreement with a previous genetic study showing a loose linkage between the OLA complex and the OLX locus.

The major histocompatibility complex of sheep (OLA) and two minor loci.

Among 11 lymphocyte factors defined in sheep, 9 are the products of multiple alleles at 2 closely linked loci: OLA-A and OLA-B. A tenth factor is the product of a gene at a third locus: OL-X probably on the same chromosome, but in this case very distant from OLA. The last factor is the product of a gene at a fourth locus: OL-Z, independent of OLA-A and B.

The OLA major histocompatibility complex of sheep. Study of six new factors and evidence of a third locus of the complex: OLA-C.

6 new factors and 2 specificities 8L (A8-like) and 6L (B6-like) are described in sheep, in addition to the previously described 11 factors. 3 new factors are the products of three alleles (C14, C15, C17) at a third OLA-C locus of the OLA major histocompatibility complex, closely linked to the OLA-A and B loci. 2 other factors are the products of 2 alleles (A13 and B12) at OLA-A and B loci. The last new factor (16) is also the product of an OLA gene, the locus of which is not yet defined. An additional 8L factor is defined as the product of an OLA-A or B new allele. On the whole, 18 factors now known in sheep are the products of genes at 5 loci. 16 factors are distributed in 3 allelic series corresponding to the 3 OLA-A, B and C loci (the last 2 factors depend each on one of the two loci OL-X and OL-Z). 28 haplotypes are described in the studied 'Préalpe' flock. The new factors identify 6 haplotypes which were previously undetermined, and they subdivide some previously described haplotypes; nevertheless, OLA genetic structure appears to have changed little in the flock for 10 years. Genes at the three OLA loci are in linkage disequilibrium.

[The major OLA histocompatibility complex of sheep. Recent results in the genetic study of 11 factors previously defined by microlymphocytotoxicity]. / Le complexe majeur d'histocompatibilité OLA du mouton. Nouveaux résultats dans l'étude génétique de 11 facteurs précédemment décrits grâce a la microlymphocytotoxicité.

The genetic study of 11 lymphocyte factors previously described in sheep was continued. 9 factors are the products of alleles at two closely linked loci OLA-A and B. The last two factors are the products of two genes at two distinct loci OL-X and OL-Z. Recombinations between the two closely linked loci are very rare (0.6%); but they are frequent between these two loci and OL-X (26%). The OL-Z locus seems to be independent of the two linked loci OLA-A and B. The allele frequencies at the four loci are given.

Sheep major histocompatibility complex OLA: gene frequencies in two French breeds with scrapie. Evidence for a linkage between OLA and resistance or susceptibility to the disease.

Gene frequencies of 13 sheep lymphocyte factors (11 factors controlled by the sheep OLA complex including three closely linked loci, and two factors by two minor loci) were compared in 189 sheep of two breeds: a. infected with scrapie, b. healthy in a contaminated environment, and c., normal. In a and c, OLA gene frequencies were similar. In healthy sheep in a contaminated environment (b), some OLA gene frequencies were higher in one breed and lower in the other. In each breed, three antigens had their frequencies significantly modified; two of them were the same in the two breeds, but they showed an inverse variation. Thus, the relative risk of clinical scrapie decreased in one breed and increased in the other for the same OLA gene. These data indicate first, that OLA antigens are not directly involved in causing scrapie, and second, that the OLA complex is linked to at least one scrapie resistance/susceptibility locus. In practice, it should be possible to select more resistent sheep, using some OLA antigens but an investigation of the OLA genes and the resistance to scrapie in a given breed is necessary before the selection.

[Major OLA histocompatibility complex of sheep. Frequency of factors in sheep affected by trembling (scrapie) or normal sheep]. / Le complexe majeur d'histocompatibilité OLA du mouton. Fréquence des facteurs chez des Ovins atteints ou non de tremblante (scrapie).

The OLA histocompatibility complex of sheep was studied in a flock of Ile-de France breed affected with Scrapie. On the whole, gene frequencies of 9 out of 11 factors were increased in the non-affected sheep of this contaminated flock. In these sheep, frequencies of the three following genes appeared to be increased significantly: OLA-A4, OLA-A8, OLA-B6. When these genes were present in the sheep of this flock, the relative risk of Scrapie was estimated at 0.05, 0.10 and 0.25, respectively.

Sheep histocompatibility antigens: a population level comparison between lymphocyte antigens previously defined in France, England and Scotland, and sheep red cell groups.

A comparison test was performed to look for correlations between the three nomenclature systems for sheep histocompatibility antigens which have been previously described in France, England and Scotland. 187 French sheep from a wide variety of breeds were typed for lymphocyte antigens with antisera which detect the OLA, P and ED series of antigens; they were also tested against 387 uncharacterized French antisera. Six clusters of sera were found which showed correspondence between antigens of at least two of the three nomenclatures; five of these clusters gave high r values of 0.78-0.94. New antisera from French sheep were found which contributed to the above clusters but few additional clusters were noted. No correlation was found between any of the lymphocyte groups of antisera tested and the sheep red cell antigens which were also tested.

[Ovine histocompatibility complex OLA and enzymatic markers in hamster X sheep hybrids. I. Asynteny between PGM3-ME1 and OLA. (author's transl)]. / Complexe d'histocompatibilité ovin (ola) et marqueurs enzymatiques dans des hybrides hamster x mouton. I. Asynténie entre PGM3-ME1 et OLA.

Eighteen independent hamster X sheep fibroblast hybrids have been obtained. OLA typing of parental cells has shown that ovine fibroblasts carry the OLA A1, A8, B7, and B9 specificities. Analysis of the segregation of the OLA genes compared with the segregation of the 16 enzymatic markers studied previously indicated that, in contrast to the situation and man and certain other mammals, the genes of the histocompatibility complex of ovines (OLA) and those coding for the enzymes PGM3 and and ME1 are asyntenic. No synteny between OLA and any other enzymatic marker studied has been established.

[The OLA major histocompatibility complex of sheep. Genetic frequencies compared in Prélpe sheep with and without scrapie]. / Le complexe majeur d'histocompatibilité OLA des ovins. Fréquences géniques comparées chez des moutons Préalpes atteints ou non de tremblante (scrapie).

The OLA genic frequencies were studied in both normal "Préalpe" Sheep and those affected with Scrapie. In the non-affected Sheep of contaminated flocks, frequencies were generally decreased, compared with frequencies of the same factors in sick Sheep or in non-infected controls. Three OLA-A genes significantly decreased; at this locus, results in "Préalpe" and "Ile-de-France" Sheep were inversed. This observation excludes OLA genes being involved in pathogeny or resistance to the disease, but suggests the existence of a linkage between the OLA loci and at least one resistance or susceptibility locus.