Analysis of 15 novel full-length BK virus sequences from three individuals: evidence of a high intra-strain genetic diversity
Open Access
- 1 September 2004
- journal article
- research article
- Published by Microbiology Society in Journal of General Virology
- Vol. 85 (9), 2651-2663
- https://doi.org/10.1099/vir.0.79920-0
Abstract
To determine the variability of BK virus (BKV)in vivo, the sequences of nine full-length molecular clones from the striated muscle and heart DNA of a patient with BKV-associated capillary leak syndrome (BKVCAP), as well as three clones each from the urine of one human immunodeficiency virus type 2-positive (BKVHI) and one healthy control subject (BKVHC), were analysed. The regulatory region of all clones corresponded to the archetypal regulatory region usually found in urine isolates. Analysis of the predicted conformation of BKVCAPproteins did not suggest any structural differences on the surface of the viral particles compared with BKVHIand BKVHCclones. No amino acid changes common to most BKVCAPclones could be identified that have not already been reported in non-vasculotropic strains. However, the coding region of each clone had unique nucleotide substitutions, and intra-host variability was greater among BKVCAPclones, with a mean difference of 0·29 % per site compared with 0·16 % for BKVHIand 0·14 % for BKVHC. The clones from each strain formed monophyletic clades, suggesting a single source of infection for each subject. The most divergent BKVCAPclones differed at 0·55 % of sites, implying a rate of nucleotide substitution of approximately 5×10−5substitutions per site per year, which is two orders of magnitude faster than estimated for the other human polyomavirus, JC virus.This publication has 45 references indexed in Scilit:
- Prospective Study of Polyomavirus Type BK Replication and Nephropathy in Renal-Transplant RecipientsThe New England Journal of Medicine, 2002
- High-fidelity PCR amplification of infectious copies of the complete simian virus 40 genome from plasmids and virus-infected cell lysatesGene, 1997
- Noncoding control region of naturally occurring BK virus variants: Sequence comparison and functional analysisVirus Genes, 1995
- Prevalence and distribution of BK virus subtypes in healthy people and immunocompromised patients detected by PCR-restriction enzyme analysisClinical and Diagnostic Virology, 1995
- CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choiceNucleic Acids Research, 1994
- Serological typing scheme for bk‐like isolates of human polyomavirusJournal of Medical Virology, 1989
- Genome Analysis of BK (WW) Viral DNA Cloned Directly from Human UrineIntervirology, 1984
- Evolutionary changes of nucleotide sequences of papova viruses BKV and SV40: They are possibly hybridsJournal of Molecular Evolution, 1982
- Human papovavirus isolated from urine of a child with acute tonsillitis.BMJ, 1981
- Isolation of a variant of BK virus with altered restriction endonuclease patternArchiv für die gesamte Virusforschung, 1978