| 1. |
- Liljeqvist, Jan-Åke, 1954, et al.
(author)
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Asymptomatically shed recombinant herpes simplex virus type 1 strains detected in saliva
- 2009
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In: Journal of General Virology. - : Microbiology Society. - 0022-1317 .- 1465-2099. ; 90:Pt 3, s. 559-66
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Journal article (peer-reviewed)abstract
- Herpes simplex virus type 1 (HSV-1) is a ubiquitous pathogen infecting most individuals worldwide. The majority of HSV-1-infected individuals have no clinical symptoms but shed HSV-1 asymptomatically in saliva. Recent phylogenetic analyses of HSV-1 have defined three genetic clades (A-C) and recombinants thereof. These data have all been based on clinical HSV-1 isolates and do not cover genetic variation of asymptomatically shed HSV-1. The primary goal of this study was to investigate such variation. A total of 648 consecutive saliva samples from five HSV-1-infected volunteers was collected. Asymptomatic shedding was detected on 7.6 % of the days from four subjects. The HSV-1 genome loads were quantified with real-time PCR and varied from 1x10(2) to 2.8x10(6) copies of virus DNA (ml saliva)(-1). Phylogenetic network analyses and bootscanning were performed on asymptomatically shed HSV-1. The analyses were based on DNA sequencing of the glycoprotein I gene, and also of the glycoprotein E gene for putative recombinants. For two individuals with clinical HSV-1 infection, the same HSV-1 strain was shed asymptomatically as induced clinical lesions, and sequence analyses revealed that these strains clustered distinctly to clades A and B, respectively. For one of the subjects with no clinical HSV-1 infection, a recombinant strain was identified. The other truly asymptomatic individual shed evolutionarily distinct HSV-1 strains on two occasions. The first strain was classified as a recombinant and the other strain clustered in clade A. High replication rates of different strains in the same person may facilitate the creation of recombinant clinical HSV-1 strains.
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| 2. |
- Norberg, Peter, 1974, et al.
(author)
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Complete-genome phylogenetic approach to varicella-zoster virus evolution: genetic divergence and evidence for recombination.
- 2006
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In: Journal of virology. - 0022-538X. ; 80:19, s. 9569-76
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Journal article (peer-reviewed)abstract
- Recent studies of varicella-zoster virus (VZV) DNA sequence variation, involving large numbers of globally distributed clinical isolates, suggest that this virus has diverged into at least three distinct genotypes designated European (E), Japanese (J), and mosaic (M). In the present study, we determined and analyzed the complete genomic sequences of two M VZV strains and compared them to the sequences of three E strains and two J strains retrieved from GenBank (including the Oka vaccine preparation, V-Oka). Except for a few polymorphic tandem repeat regions, the whole genome, representing approximately 125,000 nucleotides, is highly conserved, presenting a genetic similarity between the E and J genotypes of approximately 99.85%. These analyses revealed that VZV strains distinctly segregate into at least four genotypes (E, J, M1, and M2) in phylogenetic trees supported by high bootstrap values. Separate analyses of informative sites revealed that the tree topology was dependent on the region of the VZV genome used to determine the phylogeny; collectively, these results indicate the observed strain variation is likely to have resulted, at least in part, from interstrain recombination. Recombination analyses suggest that strains belonging to the M1 and M2 genotypes are mosaic recombinant strains that originated from ancestral isolates belonging to the E and J genotypes through recombination on multiple occasions. Furthermore, evidence of more recent recombination events between M1 and M2 strains is present in six segments of the VZV genome. As such, interstrain recombination in dually infected cells seems to figure prominently in the evolutionary history of VZV, a feature it has in common with other herpesviruses. In addition, we report here six novel genomic targets located in open reading frames 51 to 58 suitable for genotyping of clinical VZV isolates.
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| 3. |
- Norberg, Peter, 1974, et al.
(author)
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Divergence and recombination of clinical herpes simplex virus type 2 isolates.
- 2007
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In: Journal of virology. - 1098-5514. ; 81:23, s. 13158-67
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Research review (peer-reviewed)abstract
- Herpes simplex virus type 2 (HSV-2) infects the genital mucosa and is one of the most common sexually transmitted viruses. Here we sequenced a segment comprising 3.5% of the HSV-2 genome, including genes coding for glycoproteins G, I, and E, from 27 clinical isolates from Tanzania, 10 isolates from Norway, and 10 isolates from Sweden. The sequence variation was low compared to that described for clinical HSV-1 isolates, with an overall similarity of 99.6% between the two most distant HSV-2 isolates. Phylogenetic analysis revealed a divergence into at least two genogroups arbitrarily designated A and B, supported by high bootstrap values and evolutionarily separated at the root. Genogroup A contained isolates collected in Tanzania, and genogroup B contained isolates collected in Tanzania and Scandinavia, implying that the genetic variability of HSV-2 is higher in Tanzania than in Scandinavia. Recombination network analysis and bootscan analysis revealed a complex pattern of phylogenetically conflicting informative sites in the sequence alignments. These signals were present in synonymous and nonsynonymous sites in all three genes and were not accumulated in specific regions, observations arguing against positive selection. Since the PHI test applied solely to synonymous sites revealed a high statistical probability of recombination, we suggest as a novel finding that homologous recombination is, as reported earlier for HSV-1 and varicella-zoster virus, a prominent feature in the evolution of HSV-2.
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| 4. |
- Norberg, Peter, 1974
(author)
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Evolution of human alpha-herpesviruses
- 2007
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Doctoral thesis (other academic/artistic)abstract
- Herpesviridae is a large virus family with more than 100 members, which are highly disseminated among animals. Three sub-families have been classified; alpha-herpesviruses, beta-herpesviruses and gamma-herpesviruses. Eight herpesviruses have hitherto been identified in humans of which three belong to the alpha-herpesviruses; (i) herpes simplex virus type 1 (HSV-1), which is a ubiquitous pathogen causing mainly oral or genital lesions, (ii) herpes simplex virus type 2 (HSV-2), which is closely related to HSV-1, and is the most common sexually transmitted virus globally, causing mainly genital lesions, and (iii) Varicella zoster virus (VZV), which is the cause of chicken pox and shingles. All alpha-herpesviruses give lifelong infections and establish latency in the sensory ganglia. In the present work, the genetic variability of clinical HSV-1, HSV-2 and VZV isolates was investigated. Twenty-eight clinical HSV-1 isolates were collected from patients suffering from oral or genital lesions or encephalitis and compared with the laboratory strains F, KOS321 and 17. Phylogenetic analyses based on the genes US4, US7 and US8 divided the isolates into three genogroups, arbitrarily designated as A, B and C, differing in DNA sequences by approximately 2%. In addition, seven clinical isolates as well as strain 17 were classified as recombinants. To facilitate further genotyping of clinical isolates an assay was developed based on restriction enzyme cleavage of PCR-products. Furthermore, a polymorphic tandem repeat (TR) region was detected in US7. The region encodes the amino acids serine, threonine and proline, which are targets for O-linked glycosylation. Using a synthetic peptide, containing two of the repeated blocks, it was shown that the described TR-region is a substrate for massive O-linked glycosylation, and hence codes for a mucin region. Mucin regions have not been described previously within herpesvirus-encoded proteins. The corresponding genes were sequenced and investigated for 45 clinical HSV-2 isolates collected in Sweden, Norway and Tanzania. Phylogenetic analysis revealed a divergence of the isolates in one Tanzanian and one European genogroup, arbitrarily designated as A and E, differing by approximately 0.4%. In addition, analyses using recombination networks, the BootsScan method and the phi-test, suggested that most HSV-2 isolates are mosaic recombinants. The complete genome was sequenced for two VZV isolates and compared with the laboratory strains MSP, Dumas, BR, p-Oka and the vaccine strain v-Oka. The results show a division of VZV into four genogroups, designated as E, J, M1 and M2, of which M1 and M2 were suggested to be recombinants derived from ancient recombination events between viruses from the E and J genogroups. In conclusion, the results presented here demonstrate that clinical isolates, for all three investigated human alpha-herpesviruses, can be divided into different genogroups. Estimations of evolutionary timescales suggest that the divergence of the three HSV-1 genogroups may have occurred approximately 500,000 Myears BP, i.e. prior to the emergence of Homo sapiens. Furthermore, it is evident that intrastrain recombination is a prominent feature of the evolutionary history of these viruses. Thus, homologous recombination is suggested to be a powerful evolutionary mechanism for human alpha-herpesviruses to exchange genetic segments between different viral strains, as well as to create variability of TR-regions.
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| 5. |
- Norberg, Peter, 1974, et al.
(author)
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Genotyping of clinical herpes simplex virus type 1 isolates by use of restriction enzymes.
- 2006
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In: Journal of clinical microbiology. - 0095-1137. ; 44:12, s. 4511-4
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Journal article (peer-reviewed)abstract
- Recently, three distinct genotypes of clinical herpes simplex virus type 1 (HSV-1) isolates were identified based on DNA sequence information and phylogenetic analysis of clinical isolates and laboratory strains. We utilized single-nucleotide polymorphism within the genes coding for glycoproteins G and I for rapid genotype classification by PCR and restriction enzyme cleavage. The method is suitable for high-scale genotyping of clinical HSV-1 isolates and for the detection of recombinants.
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| 6. |
- Norberg, Peter, 1974, et al.
(author)
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Glycoprotein I of herpes simplex virus type 1 contains a unique polymorphic tandem-repeated mucin region.
- 2007
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In: The Journal of general virology. - : Microbiology Society. - 0022-1317 .- 1465-2099. ; 88:Pt 6, s. 1683-8
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Research review (peer-reviewed)abstract
- Glycoprotein I (gI) of herpes simplex virus type 1 (HSV-1) contains a tandem repeat (TR) region including the amino acids serine and threonine, residues that can be utilized for O-glycosylation. The length of this TR region was determined for 82 clinical HSV-1 isolates and the results revealed a polymorphic distribution of two to six or eight repeated blocks with a majority harbouring between two and four repeats. Assessment of the O-glycosylation capacity of an acceptor peptide (STPSTTTSTPSTTT), representing two of the gI blocks, showed that the peptide was a universal substrate for O-glycosylation not only for the two most commonly expressed N-acetyl-d-galactosamine (GalNAc)-T1 and -T2 transferases, but also for the GalNAc-T3, -T4 and -T11 transferases. Immunoblotting of virus-infected cells showed that gI was exclusively O-glycosylated with GalNAc monosaccharides (Tn antigen). A polymorphic mucin region has not been described previously for HSV-1 and is a unique finding, as repeated blocks within gI homologues are lacking in other alphaherpesviruses.
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| 7. |
- Norberg, Peter, 1974
(author)
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Prevalence of herpes simplex virus type 1 glycoprotein G (gG) and gI genotypes in patients with herpetic keratitis.
- 2008
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In: The british journal of ophthalmology. - : BMJ. - 0007-1161. ; 92:9, s. 1195-200
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Journal article (peer-reviewed)abstract
- AIM: Recent phylogenetic analyses on the herpes simplex virus type 1 (HSV-1) genes US4, encoding glycoprotein G (gG) and US7, encoding gI, of clinical HSV-1 isolates have led to the classification of HSV-1 into three genotypes, arbitrarily designated as A, B and C. The prevalence of the HSV-1 gG and gI genotypes and their potential disease association was determined in a large cohort of patients with herpetic keratitis (HK). METHODS: Primary corneal HSV-1 isolates of 178 HK patients were genotyped by a PCR-based restriction fragment length polymorphism method targeting the viral genes US4 and US7. RESULTS: Genotype B was more frequently expressed by the corneal HSV-1 isolates compared with genotypes A and C. Fifty-five of 178 corneal isolates (31%) had different genotypes in both loci. No clinically relevant associations were observed between the HSV-1 genotypes and disease outcome in the HK patients studied. CONCLUSIONS: The data presented demonstrate a high frequency of recombinant corneal HSV-1 isolates and suggest that clinical outcome of HSV-1-induced keratitis is independent of a gG or gI genotype.
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