Genotypes of JC virus in East, Central and Southwest Europe

Abstract

Distinctive genotypes of JC virus have been described for the major continental landmasses. Studies on European-Americans and small cohorts in Europe showed predominantly Type 1. Types 2 and 7 are found in Asia, and Types 3 and 6 in Africa. These genotypes differ in sequence by about 1-3 %. Each genotype may have several subtypes which differ from each other by about 0n5-1 %. The genotypes can be defined by a distinctive pattern of nucleotides in a typing region of the VP1 gene. This genotyping approach has been confirmed by phylogenetic reconstruction using the entire genome exclusive of the rearranging regulatory region. In this first large European study, we report on the urinary excretion of JCV DNA of 350 individuals from Poland, Hungary, Germany and Spain. We included Gypsy cohorts in Hungary (Roma), Germany (Sinti), and Spain (Gitano), as well as Basques in Spain. We show that while Type 1 predominates in Europe, the proportions of Type 1A and 1B may differ from East to Southwest Europe. Type 4, closely related to the Type 1 sequence (only "1 % difference) was a minor genotype in Germany, Poland and Spain, but represented the majority in Basques. The Gitanos in Spain showed a variant Type 4 sequence termed ' Rom-1 '. Interestingly, neither the Gitanos in Spain, nor Sinti or Roma in Germany or Hungary showed the Type 2 or Type 7 genotype that might be expected if their origins were in an Asian population.

Archetype and Rearranged Non-coding Control Regions in Urothelial Bladder Carcinoma of Immunocompetent Individuals

“…In particular, the 217-G to A nucleotide transition inside the box F was isolated within the NCCR sequences of patients with European genotypes. In fact, this point mutation seems to be a common feature of the European strains and was also found in European Americans (60). Indeed in our study, there was a prevalence of the European genotypes 1A, 1B and 4, followed by the East African genotype 3A.…”

“…All these changes corresponded to known sequence polymorphisms (28,59,60). Moreover, the nucleotide variations G108A and A133C did not involve any cellular transcriptional factor binding site, whereas the nucleotide substitutions G95C and G217A involved the binding sites for TAR and NF1, respectively (Figure 3).…”

The human JC polyomavirus (JCPyV): virological background and clinical implications

“…Second, the European and European American types JCPyV genotype 1A and 1B deviate from the VP1 consensus and show the following amino acids at positions 75R, 117S, 158L, 245K, and 74S, 117S, 126A, respectively (17).…”

Phylogenetic Analysis of Polyomavirus Simian Virus 40 from Monkeys and Humans Reveals Genetic Variation

“…Abbreviations: G, the whole genomic data set; Gϩ, 100 additional bootstrap replicate trees of the genomic data set; TAG, the T-ag-C data set for the same taxa; TAG5th, the T-ag-C data set for the same taxa, treating gaps as a fifth character; RND, a comparison of two sets of randomly generated trees. Prior to this analysis, phylogenetic studies of whole genomes of polyomaviruses had been performed only for JC virus (1)(2)(3)19). The results obtained for SV40 are similar in that genotypes can be distinguished by analyzing a genomic region with sequence variability outside the viral regulatory region.…”