Sequence variation of Epstein-Barr virus: viral types, geography, codon usage and diseases

138 new Epstein-Barr virus (EBV) genome sequences have been determined. 125 of these and 116 from previous reports were combined to produce a multiple sequence alignment of 241 EBV genomes, which we have used to analyze variation within the viral genome. The type 1/type2 classification of EBV remains the major form of variation and is defined mostly by EBNA2 and EBNA3, but the type 2 SNPs at the EBNA3 locus extend into the adjacent gp350 and gp42 genes, whose products mediate infection of B cells by EBV. A small insertion within the BART miRNA region of the genome was present in 21 EBV strains. EBV from saliva of USA patients with chronic active EBV infection aligned with the wild type EBV genome, with no evidence of WZhet rearrangements. The V3 polymorphism in the Zp promoter for BZLF1 was found to be frequent in nasopharyngeal carcinoma cases both from Hong Kong and Indonesia. Codon usage was found to differ between latent and lytic cycle EBV genes and the main forms of variation of the EBNA1 protein have been identified.IMPORTANCE Epstein-Barr virus causes most cases of infectious mononucleosis and post-transplant lymphoproliferative disease. It contributes to several types of cancer including Hodgkin's lymphoma, Burkitt's lymphoma, diffuse large B cell lymphoma, nasopharyngeal carcinoma and gastric carcinoma. EBV genome variation is important because some of the diseases associated with EBV have very different incidences in different populations and geographic regions - differences in the EBV genome might contribute to these diseases. Some specific EBV genome alterations that appear to be significant in EBV associated cancers are already known and current efforts to make an EBV vaccine and antiviral drugs should also take account of sequence differences in the proteins used as targets

Inter-examiner reliability of the diagnosis of cervical pillar hyperplasia (CPH) and the correlation between CPH and spinal degenerative joint disease (DJD)

BACKGROUND: Cervical pillar hyperplasia (CPH) is a recently described phenomenon of unknown aetiology. Its clinical importance is poorly understood at the present time; therefore, the objective of this study was to determine (1) the inter-examiner reliability of detecting CPH and (2) if there is a clinically important correlation (r > 0.4) between the number of cervical spine levels showing signs of degenerative joint disease (DJD) and CPH. METHODS: The sample consisted of 320 radiographs of human male and female subjects who ranged from 40 to 79 years of age. The inter-examiner reliability of assessing the presence/absence of pillar hyperplasia was evaluated on 50 neutral lateral radiographs by two examiners using line drawings and it was quantified using the kappa coefficient of concordance. To determine the presence/absence of hyperplastic pillars as well as the presence/absence of DJD at each intervertebral disc and zygapophysial joint, 320 AP open mouth, AP lower cervical and neutral lateral radiographs were then examined. The unpaired t-test at the 5% level of significance was performed to test for a statistically significant difference between the number of levels affected by DJD in patients with and without hyperplasia. The Spearman's rho at the 5% level of significance was performed to quantify the correlation between DJD and age. RESULTS: The inter-examiner reliability of detecting cervical pillar hyperplasia was moderate with a kappa coefficient of 0.51. The unpaired t-test indicated that there was no statistically significant difference (p > 0.05) between the presence/absence of cervical pillar hyperplasia and the number of levels affected by DJD in an age-matched population, regardless of whether all elements were considered together, or the discs and facets were analyzed separately. A Spearman correlation rank of 0.67 (p < 0.05) suggested a moderately strong correlation between the number of elements (i.e. discs/facets) affected, and the age of the individual. CONCLUSION: Cervical pillar hyperplasia is a reasonable concept that requires further research. Its evaluation is easy to learn and acceptably reliable. Previous research has suggested that CPH may affect the cervical lordosis, and therefore, alter biomechanics which may result in premature DJD. This current study, however, indicates that, globally, CPH does not appear to be related to the development of DJD

Dynamics of an Infectious Keratoconjunctivitis Outbreak by Mycoplasma conjunctivae on Pyrenean Chamois Rupicapra p. pyrenaica

Between 2006 and 2008, an outbreak of Infectious Keratoconjunctivitis (IKC) affected Pyrenean chamois Rupicapra p. pyrenaica, an endemic subspecies of mountain ungulate that lives in the Pyrenees. The study focused on 14 mountain massifs (180,000 ha) where the species’ population is stable. Cases of IKC were detected in ten of the massifs and, in five of them, mortality was substantial. The outbreak spread quickly from the first location detected, with two peaks in mortality that affected one (2007) and three (2008) massifs. In the latter, the peak was seasonal (spring to autumn) and, in the former, the outbreak persisted through winter. To identify the outbreak’s aetiology, we examined 105 Pyrenean chamois clinically affected with IKC. TaqMan rt-PCR identified Mycoplasma conjunctivae in 93 (88.5%) of the chamois. Another rt-PCR detected Chlamydophila spp. in 14 of chamois, and 12 of those had mixed infections with mycoplasmas. In the period 2000–2007, the chamois population increased slightly (λ 1.026) but decreased significantly during the IKC outbreak (λ 0.8, 2007–2008; λ 0.85, 2008–2009) before increasing significantly after the outbreak (λ 1.1, 2009–2010). Sex-biased mortality shifted the adult sex ratio toward males (from 0.6 to 0.7 males per female) and reduced productivity slightly. Hunting was practically banned in the massifs where chamois experienced significant mortality and allowed again after the outbreak ended. Long-term monitoring of wild populations provides a basis for understanding the impacts of disease outbreaks and improves management decisions, particularly when species are subject to extractive exploitation