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Last AR, Pickering H, Roberts CH, Coll F, Phelan J, Burr SE, Cassama E, Nabicassa M, Seth-Smith HMB, Hadfield J, Cutcliffe LT, Clarke IN, Mabey DCW, Bailey RL, Clark TG, Thomson NR, Holland MJ. Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity. Genome Med 2018; 10:15. [PMID: 29482619 PMCID: PMC5828069 DOI: 10.1186/s13073-018-0521-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 02/13/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Chlamydia trachomatis (Ct) is the most common infectious cause of blindness and bacterial sexually transmitted infection worldwide. Ct strain-specific differences in clinical trachoma suggest that genetic polymorphisms in Ct may contribute to the observed variability in severity of clinical disease. METHODS Using Ct whole genome sequences obtained directly from conjunctival swabs, we studied Ct genomic diversity and associations between Ct genetic polymorphisms with ocular localization and disease severity in a treatment-naïve trachoma-endemic population in Guinea-Bissau, West Africa. RESULTS All Ct sequences fall within the T2 ocular clade phylogenetically. This is consistent with the presence of the characteristic deletion in trpA resulting in a truncated non-functional protein and the ocular tyrosine repeat regions present in tarP associated with ocular tissue localization. We have identified 21 Ct non-synonymous single nucleotide polymorphisms (SNPs) associated with ocular localization, including SNPs within pmpD (odds ratio, OR = 4.07, p* = 0.001) and tarP (OR = 0.34, p* = 0.009). Eight synonymous SNPs associated with disease severity were found in yjfH (rlmB) (OR = 0.13, p* = 0.037), CTA0273 (OR = 0.12, p* = 0.027), trmD (OR = 0.12, p* = 0.032), CTA0744 (OR = 0.12, p* = 0.041), glgA (OR = 0.10, p* = 0.026), alaS (OR = 0.10, p* = 0.032), pmpE (OR = 0.08, p* = 0.001) and the intergenic region CTA0744-CTA0745 (OR = 0.13, p* = 0.043). CONCLUSIONS This study demonstrates the extent of genomic diversity within a naturally circulating population of ocular Ct and is the first to describe novel genomic associations with disease severity. These findings direct investigation of host-pathogen interactions that may be important in ocular Ct pathogenesis and disease transmission.
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Affiliation(s)
- A. R. Last
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - H. Pickering
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - C. h. Roberts
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - F. Coll
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - J. Phelan
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - S. E. Burr
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, Fajara, Gambia
| | - E. Cassama
- Programa Nacional de Saúde de Visão, Ministério de Saúde Publica, Bissau, Guinea-Bissau
| | - M. Nabicassa
- Programa Nacional de Saúde de Visão, Ministério de Saúde Publica, Bissau, Guinea-Bissau
| | - H. M. B. Seth-Smith
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Clinical Microbiology, Universitätsspital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - J. Hadfield
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - L. T. Cutcliffe
- Molecular Microbiology Group, University of Southampton Medical School, Southampton, UK
| | - I. N. Clarke
- Molecular Microbiology Group, University of Southampton Medical School, Southampton, UK
| | - D. C. W. Mabey
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - R. L. Bailey
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - T. G. Clark
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - N. R. Thomson
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - M. J. Holland
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
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O’Neill CE, Seth-Smith HMB, Van Der Pol B, Harris SR, Thomson NR, Cutcliffe LT, Clarke IN. Chlamydia trachomatis clinical isolates identified as tetracycline resistant do not exhibit resistance in vitro: whole-genome sequencing reveals a mutation in porB but no evidence for tetracycline resistance genes. Microbiology (Reading) 2013; 159:748-756. [DOI: 10.1099/mic.0.065391-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- C. E. O’Neill
- Faculty of Medicine, CES Academic Unit, Level C, South Block, University of Southampton, Southampton General Hospital, Tremona Road, Southampton, UK
| | - H. M. B. Seth-Smith
- The Wellcome Trust Sanger Institute, Pathogen Genomics, Hinxton, Cambridge, UK
| | - B. Van Der Pol
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - S. R. Harris
- The Wellcome Trust Sanger Institute, Pathogen Genomics, Hinxton, Cambridge, UK
| | - N. R. Thomson
- The Wellcome Trust Sanger Institute, Pathogen Genomics, Hinxton, Cambridge, UK
| | - L. T. Cutcliffe
- Faculty of Medicine, CES Academic Unit, Level C, South Block, University of Southampton, Southampton General Hospital, Tremona Road, Southampton, UK
| | - I. N. Clarke
- Faculty of Medicine, CES Academic Unit, Level C, South Block, University of Southampton, Southampton General Hospital, Tremona Road, Southampton, UK
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Hussey RJ, Coates L, Gill RS, Wright JN, Sarwar M, Coker S, Erskine PT, Cooper JB, Wood S, Clarke IN, Lambden PR, Broadbridge R, Shoolingin-Jordan PM. Crystallization and preliminary X-ray diffraction analysis of the protease from Southampton norovirus complexed with a Michael acceptor inhibitor. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1544-8. [PMID: 21045318 PMCID: PMC3001671 DOI: 10.1107/s1744309110039059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Accepted: 09/29/2010] [Indexed: 11/10/2022]
Abstract
Noroviruses are the predominant cause of human epidemic nonbacterial gastroenteritis. Viral replication requires a cysteine protease that cleaves a 200 kDa viral polyprotein into its constituent functional parts. Here, the crystallization of the recombinant protease from the Southampton norovirus is described. Whilst the native crystals were found to diffract only to medium resolution (2.9 Å), cocrystals of an inhibitor complex diffracted X-rays to 1.7 Å resolution. The polypeptide inhibitor (Ac-EFQLQ-propenyl ethyl ester) possesses an amino-acid sequence designed to match the substrate specificity of the enzyme, but was synthesized with a reactive Michael acceptor group at the C-terminal end.
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Affiliation(s)
- R. J. Hussey
- School of Biological Sciences, University of Southampton, Southampton SO16 7PX, England
| | - L. Coates
- Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - R. S. Gill
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Department of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - J. N. Wright
- School of Biological Sciences, University of Southampton, Southampton SO16 7PX, England
| | - M. Sarwar
- School of Biological Sciences, University of Southampton, Southampton SO16 7PX, England
| | - S. Coker
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Department of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - P. T. Erskine
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Department of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - J. B. Cooper
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Department of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - S. Wood
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Department of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - I. N. Clarke
- Molecular Microbiology Group, Division of Infection, Inflammation and Immunity, University Medical School, Southampton General Hospital, Southampton SO16 6YD, England
| | - P. R. Lambden
- Molecular Microbiology Group, Division of Infection, Inflammation and Immunity, University Medical School, Southampton General Hospital, Southampton SO16 6YD, England
| | - R. Broadbridge
- Peptide Protein Research Ltd, E2 Knowle Village Business Park, Wickham, Hants PO17 5DY, England
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Oliver SL, Wood E, Asobayire E, Wathes DC, Brickell JS, Elschner M, Otto P, Lambden PR, Clarke IN, Bridger JC. Serotype 1 and 2 bovine noroviruses are endemic in cattle in the United kingdom and Germany. J Clin Microbiol 2007; 45:3050-2. [PMID: 17596356 PMCID: PMC2045281 DOI: 10.1128/jcm.02015-06] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genomically and antigenically distinct bovine noroviruses Bo/Jena/1980/DE and Bo/Newbury2/1976/UK have been associated with calf diarrhea. In the present seroprevalence study, both were found to be endemic in cattle from Germany and the United Kingdom, a finding in contrast to previous virus prevalence studies. They were less common than group A rotaviruses, particularly in calves, suggesting a different epidemiology.
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Affiliation(s)
- S L Oliver
- Department of Pathology and Infectious Diseases, Royal Veterinary College, 4 Royal College Street, London NW1 0TU, United Kingdom
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Skilton RJ, Cutcliffe LT, Pickett MA, Lambden PR, Fane BA, Clarke IN. Intracellular parasitism of chlamydiae: specific infectivity of chlamydiaphage Chp2 in Chlamydophila abortus. J Bacteriol 2007; 189:4957-9. [PMID: 17468245 PMCID: PMC1913433 DOI: 10.1128/jb.00235-07] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The obligate intracellular nature of chlamydiae presents challenges to the characterization of its phages, which are potential tools for a genetic transfer system. An assay for phage infectivity is described, and the infectious properties of phage Chp2 were determined.
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Affiliation(s)
- R J Skilton
- Molecular Microbiology Group, University Medical School, Southampton General Hospital, Southampton, United Kingdom
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Oliver SL, Batten CA, Deng Y, Elschner M, Otto P, Charpilienne A, Clarke IN, Bridger JC, Lambden PR. Genotype 1 and genotype 2 bovine noroviruses are antigenically distinct but share a cross-reactive epitope with human noroviruses. J Clin Microbiol 2006; 44:992-8. [PMID: 16517888 PMCID: PMC1393167 DOI: 10.1128/jcm.44.3.992-998.2006] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bovine enteric caliciviruses Bo/Jena/1980/DE and Bo/Newbury2/1976/UK represent two distinct genotypes within a new genogroup, genogroup III, in the genus Norovirus of the family Caliciviridae. In the present study, the antigenic relatedness of these two genotypes was determined for the first time to enable the development of tests to detect and differentiate between both genotypes. Two approaches were used. First, cross-reactivity was examined by enzyme-linked immunosorbent assay (ELISA) using recombinant virus-like particles (VLPs) and convalescent-phase sera from calves infected with either Jena (genotype 1) or Newbury2 (genotype 2). Second, cross-reactivity was examined between the two genotypes with a monoclonal antibody, CM39, derived using Jena VLPs. The two genotypes, Jena and Newbury2, were antigenically distinct with little or no cross-reactivity by ELISA to the heterologous VLPs using convalescent calf sera that had homologous immunoglobulin G titers of log10 3.1 to 3.3. CM39 reacted with both Jena and heterologous Newbury2 VLPs. The CM39 epitope was mapped to nine amino acids (31PTAGAQIAA39) in the Jena capsid protein, which was not fully conserved for Newbury2 (31PTAGAPVAA39). Molecular modeling showed that the CM39 epitope was located within the NH2-terminal arm inside the virus capsid. Surprisingly, CM39 also reacted with VLPs from two genogroup II/3 human noroviruses by ELISA and Western blotting. Thus, although the bovine noroviruses Jena and Newbury2 corresponded to two distinct antigenic types or serotypes, they shared at least one cross-reactive epitope. These findings have relevance for epidemiological studies to determine the prevalence of bovine norovirus serotypes and to develop vaccines to bovine noroviruses.
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Affiliation(s)
- S L Oliver
- Department of Pathology and Infectious Diseases, Royal Veterinary College, Camden, London, United Kingdom.
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7
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Schachter J, Stephens RS, Timms P, Kuo C, Bavoil PM, Birkelund S, Boman J, Caldwell H, Campbell LA, Chernesky M, Christiansen G, Clarke IN, Gaydos C, Grayston JT, Hackstadt T, Hsia R, Kaltenboeck B, Leinonnen M, Ocjius D, McClarty G, Orfila J, Peeling R, Puolakkainen M, Quinn TC, Rank RG, Raulston J, Ridgeway GL, Saikku P, Stamm WE, Taylor-Robinson D, Wang SP, Wyrick PB. Radical changes to chlamydial taxonomy are not necessary just yet. Int J Syst Evol Microbiol 2006. [DOI: 10.1099/00207713-56-3-677-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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8
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Vipond IB, Caul EO, Hirst D, Carmen B, Curry A, Lopman BA, Pead P, Pickett MA, Lambden PR, Clarke IN. National epidemic of Lordsdale Norovirus in the UK. J Clin Virol 2004; 30:243-7. [PMID: 15135743 DOI: 10.1016/j.jcv.2003.11.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2003] [Indexed: 10/26/2022]
Abstract
BACKGROUND In early 2002 reports of outbreaks of gastroenteritis reached unprecedented levels in the UK. Forty five Norovirus outbreaks were reported in January 2002. OBJECTIVES The objective of the study was to determine whether the outbreaks were Noroviral in origin and if so whether they represented a homogeneous or heterogeneous collection of Noroviruses by applying EIA and sequence analysis to representative faecal samples. STUDY DESIGN Faecal specimens were collected during the week of highest incidence from 21 outbreaks in a variety of health care settings including hospitals and nursing homes. The outbreaks occurred in geographically distinct regions of the UK and samples were collected by reference laboratories in Glasgow, Manchester, Bristol and Southampton. RESULTS The samples were all positive for Noroviruses by negative stain electron microscopy (EM) and Lordsdale virus (LV) EIA, therefore reverse transcriptase polymerase chain reaction (RT-PCR) amplification and nucleotide sequencing of the Norovirus RNA polymerase gene was performed on amplicons from samples of each of the 21 outbreaks to investigate the nature and extent of diversity. All samples were very closely related to the reference Lordsdale virus genome sequence. LV was first discovered during an hospital outbreak of gastroenteritis in Southampton General Hospital in March 1993. CONCLUSIONS Noroviruses are a major cause of outbreaks of gastroenteritis in health care settings. LV is the predominant Norovirus in the UK and was detected in outbreaks that occurred during the national peak of gastroenteritis reports in January 2002.
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Affiliation(s)
- I B Vipond
- Bristol Public Health Laboratory, Myrtle Road, Bristol, BS2 8EL, UK
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Abstract
The host range of phiCPAR39 is limited to four Chlamydophila species: C. abortus, C. caviae, C. pecorum, and C. pneumoniae. Chp3 (a newly discovered bacteriophage isolated from C. pecorum) shares three of these hosts (C. abortus, C. caviae, and C. pecorum) but can additionally infect Chlamydophila felis. The ability to support replication was directly correlated with the binding properties of the respective bacteriophages with their host species. Binding studies also show that phiCPAR39 and Chp3 use different host receptors to infect the same host cells: cell binding is sensitive to proteinase K treatment, confirming that the chlamydiaphage receptors are proteinaceous in nature.
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Affiliation(s)
- J S Everson
- Molecular Microbiology and Infection, University Medical School, Southampton General Hospital, Southampton, SO16 6YD, United Kingdom
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10
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Deng Y, Batten CA, Liu BL, Lambden PR, Elschner M, Günther H, Otto P, Schnürch P, Eichhorn W, Herbst W, Clarke IN. Studies of epidemiology and seroprevalence of bovine noroviruses in Germany. J Clin Microbiol 2003; 41:2300-5. [PMID: 12791840 PMCID: PMC156573 DOI: 10.1128/jcm.41.6.2300-2305.2003] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Jena virus (JV) is a bovine enteric calicivirus that causes diarrhea in calves. The virus is approximately 30 nm in diameter and has a surface morphology similar to the human Norwalk virus. The genome sequence of JV was recently described, and the virus has been assigned to the genus Norovirus of the family CALICIVIRIDAE: In the present study, the JV capsid gene encoded by open reading frame 2 was cloned into the baculovirus transfer vector pFastBac 1, and this was used to transform Escherichia coli to generate a recombinant bacmid. Transfection of insect cells with the recombinant baculovirus DNA resulted in expression of the JV capsid protein. The recombinant JV capsid protein undergoes self-assembly into virus-like particles (VLPs) similar to JV virions in size and appearance. JV VLPs were released into the cell culture supernatant, concentrated, and then purified by CsCl equilibrium gradient centrifugation. Purified JV VLPs were used to hyperimmunize laboratory animals. An antigen capture enzyme-linked immunosorbent assay (ELISA) was developed and characterized initially with clinical specimens containing defined human noroviruses and bovine diarrheal samples from calves experimentally infected with JV; the ELISA was specific only for JV. The ELISA was used to screen 381 diarrheal samples collected from dairy herds in Thuringia, Hesse, and Bavaria, Germany, from 1999 to 2002; 34 of these samples (8.9%) were positive for JV infection. The unexpectedly high prevalence of JV was confirmed in a seroepidemiological study using 824 serum or plasma samples screened using an anti-JV ELISA, which showed that 99.1% of cattle from Thuringia have antibodies to JV.
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Affiliation(s)
- Y Deng
- Molecular Microbiology Group, University Medical School, Southampton General Hospital, Southampton SO16 6YD, United Kingdom
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11
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Everson JS, Garner SA, Fane B, Liu BL, Lambden PR, Clarke IN. Biological properties and cell tropism of Chp2, a bacteriophage of the obligate intracellular bacterium Chlamydophila abortus. J Bacteriol 2002; 184:2748-54. [PMID: 11976304 PMCID: PMC135034 DOI: 10.1128/jb.184.10.2748-2754.2002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A number of bacteriophages belonging to the Microviridae have been described infecting chlamydiae. Phylogenetic studies divide the Chlamydiaceae into two distinct genera, Chlamydia and Chlamydophila, containing three and six different species, respectively. In this work we investigated the biological properties and host range of the recently described bacteriophage Chp2 that was originally discovered in Chlamydophila abortus. The obligate intracellular development cycle of chlamydiae has precluded the development of quantitative approaches to assay bacteriophage infectivity. Thus, we prepared hybridomas secreting monoclonal antibodies (monoclonal antibodies 40 and 55) that were specific for Chp2. We demonstrated that Chp2 binds both C. abortus elementary bodies and reticulate bodies in an enzyme-linked immunosorbent assay. Monoclonal antibodies 40 and 55 also detected bacteriophage Chp2 antigens in chlamydia-infected eukaryotic cells. We used these monoclonal antibodies to monitor the ability of Chp2 to infect all nine species of chlamydiae. Chp2 does not infect members of the genus Chlamydia (C. trachomatis, C. suis, or C. muridarum). Chp2 can infect C. abortus, C. felis, and C. pecorum but is unable to infect other members of this genus, including C. caviae and C. pneumoniae, despite the fact that these chlamydial species support the replication of very closely related bacteriophages.
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Affiliation(s)
- J S Everson
- Molecular Microbiology and Infection, University Medical School, Southampton General Hospital, Southampton SO16 6YD, United Kingdom
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Abstract
Within the last decade molecular analyses of the genome of Norwalk-like viruses (NLVs) have confirmed that this important group of infectious agents belongs to the Caliciviridae family. NLVs have a positive-sense, single-stranded RNA genome of approximately 7700 nucleotides excluding the polyadenylated tail. The genome encodes three open reading frames: ORF 1 is the largest (approximately 1700 amino acids) and is expressed as a polyprotein precursor that is cleaved by the viral 3C-like protease; ORF 2 encodes the viral capsid (550 amino acids); and ORF 3 encodes a small basic protein of unknown function. Comparative sequencing studies of human caliciviruses have revealed a second distinct group of viruses known as Sapporo-like viruses (SLVs). SLVs also have a single-stranded, positive-sense RNA genome of approximately 7400 nucleotides and the small 3' terminal ORF (NLV-ORF3 equivalent) is retained. Phylogenetic analyses of NLV and SLV genomic sequences have assigned these viruses to two different genera with each genus comprised of two distinct genogroups. The fundamental difference in genome organization between NLVs and SLVs is that the polyprotein and capsid ORFs are contiguous and fused in SLVs. Progress in understanding the molecular biology of human caliciviruses is hampered by the lack of a cell culture system for virus propagation. Studies on viral replication and virion structure have therefore relied on the expression of recombinant virus proteins in heterologous systems. Norwalk virus capsid expressed in insect cells assembles to form virus-like particles (VLPs). Structural studies have shown that Norwalk virus VLPs are comprised of 90 dimers of the capsid protein.
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Affiliation(s)
- I N Clarke
- Division of Cell and Molecular Medicine, University of Southampton Medical School, Southampton SO16 6YD, UK
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13
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Schachter J, Stephens RS, Timms P, Kuo C, Bavoil PM, Birkelund S, Boman J, Caldwell H, Campbell LA, Chernesky M, Christiansen G, Clarke IN, Gaydos C, Grayston JT, Hackstadt T, Hsia R, Kaltenboeck B, Leinonnen M, Ojcius D, Ocjius D, McClarty G, Orfila J, Peeling R, Puolakkainen M, Quinn TC, Rank RG, Raulston J, Ridgeway GL, Saikku P, Stamm WE, Taylor-Robinson DT, Wang SP, Wyrick PB. Radical changes to chlamydial taxonomy are not necessary just yet. Int J Syst Evol Microbiol 2001; 51:249. [PMID: 11211265 DOI: 10.1099/00207713-51-1-249] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Abstract
Small round structured viruses (SRSVs) are the major cause of outbreaks of gastroenteritis in the UK. Diagnosis is problematic due to insensitive electron microscopy (EM) or technically demanding reverse transcription polymerase chain reaction (RT-PCR) techniques. We have studied outbreaks of non-bacterial gastroenteritis using an EIA based upon recombinant capsid protein from the currently prevalent circulating strain of SRSV (Lordsdale Genotype II) and compared its performance against EM and RT-PCR assays. Faecal specimens sent to the Bristol Public Health Laboratory for outbreak investigation from December 1996 to December 1997 were applied retrospectively to the SRSV EIA and results compared with the routine EM and RT-PCR that had been carried out prospectively. Overall, the three tests identified SRSVs in specimens from 70% of the outbreaks (213/305) investigated. Of the 213 total positive outbreaks, the EIA identified 71%, that compared favourably with EM (63%) and RT-PCR (84%). The Lordsdale Genotype II SRSV EIA provides a simple cost-effective assay that will for the first time make detection of currently circulating SRSV strains associated with UK outbreaks available to all routine laboratories. The EIA format makes the assay widely applicable to non-specialist laboratories, unlike the RT-PCR assay, and the improved sensitivity over EM will allow successful screening of UK outbreaks alongside commercial EIAs currently available for adenovirus, astrovirus and rotavirus. Furthermore, the assay will allow rapid identification of emerging SRSV strains.
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Affiliation(s)
- I B Vipond
- Regional Virus Laboratory, Public Health Laboratory, Bristol, United Kingdom
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Green KY, Ando T, Balayan MS, Berke T, Clarke IN, Estes MK, Matson DO, Nakata S, Neill JD, Studdert MJ, Thiel HJ. Taxonomy of the caliciviruses. J Infect Dis 2000; 181 Suppl 2:S322-30. [PMID: 10804145 DOI: 10.1086/315591] [Citation(s) in RCA: 374] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The International Committee on Taxonomy of Viruses (ICTV) has recently approved several proposals submitted by the present Caliciviridae Study Group. These proposals include the division of the family into 4 new genera designated Lagovirus, Vesivirus, "Norwalk-like viruses (NLVs), and "Sapporo-like viruses (SLVs); the latter 2 genera were assigned temporary names until acceptable names can be determined by the scientific community. The genera have been further divided into the following species: Feline calicivirus and Vesicular exanthema of swine virus (genus Vesivirus), Rabbit hemorrhagic disease virus and European brown hare syndrome virus (genus Lagovirus), Norwalk virus (genus NLV), and Sapporo virus (genus SLV). In addition, the ICTV approved a proposal to remove the hepatitis E virus from the Caliciviridae into an "unassigned classification status.
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Affiliation(s)
- K Y Green
- National Institutes of Health, Bethesda, MD 20832, USA. kgreen@niaid. nih.gov
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Abstract
The application of molecular techniques to the characterization of caliciviruses has resulted in an extensive database of sequence information. This information has led to the identification of 4 distinct genera. The human enteric caliciviruses have been assigned to 2 of these genera. This division is reflected not only in sequence diversity but in a fundamental difference in genome organization. Complete genome sequences are now available for 5 enteric caliciviruses and demonstrate that human and animal enteric caliciviruses are phylogenetically closely related. Currently, there is no cell culture system for the human viruses; therefore, studies have relied on heterologous expression and in vitro systems. These studies have shown that in both human and animal viruses the viral nonstructural proteins are produced from a polyprotein precursor that is cleaved by a single viral protease. The purpose of this article is to provide an overview of the current knowledge of genome structure and gene expression in the enteric caliciviruses.
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Affiliation(s)
- I N Clarke
- Virology Group, University Medical School, Southampton General Hospital, Southampton, SO16 6YD, UK.
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17
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Abstract
Comparisons of the proteome of abortifacient Chlamydia psittaci isolates from sheep by two-dimensional gel electrophoresis identified a novel abundant protein with a molecular mass of 61.4 kDa and an isoelectric point of 6.41. C-terminal sequence analysis of this protein yielded a short peptide sequence that had an identical match to the viral coat protein (VP1) of the avian chlamydiaphage Chp1. Electron microscope studies revealed the presence of a 25-nm-diameter bacteriophage (Chp2) with no apparent spike structures. Thin sections of chlamydia-infected cells showed that Chp2 particles were located to membranous structures surrounding reticulate bodies (RBs), suggesting that Chp2 is cytopathic for ovine C. psittaci RBs. Chp2 double-stranded circular replicative-form DNA was purified and used as a template for DNA sequence analysis. The Chp2 genome is 4,567 bp and encodes up to eight open reading frames (ORFs); it is similar in overall organization to the Chp1 genome. Seven of the ORFs (1 to 5, 7, and 8) have sequence homologies with Chp1. However, ORF 6 has a different spatial location and no cognate partner within the Chp1 genome. Chlamydiaphages have three viral structural proteins, VP1, VP2, and VP3, encoded by ORFs 1 to 3, respectively. Amino acid residues in the phiX174 procapsid known to mediate interactions between the viral coat protein and internal scaffolding proteins are conserved in the Chp2 VP1 and VP3 proteins. We suggest that VP3 performs a scaffolding-like function but has evolved into a structural protein.
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Affiliation(s)
- B L Liu
- Department of Molecular Microbiology, University Medical School, Southampton General Hospital, Southampton SO16 6YD, United Kingdom
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18
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Pelosi E, Lambden PR, Caul EO, Liu B, Dingle K, Deng Y, Clarke IN. The seroepidemiology of genogroup 1 and genogroup 2 Norwalk-like viruses in Italy. J Med Virol 1999; 58:93-9. [PMID: 10223553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Southampton virus (SV) and Lordsdale viruses (LV) are small round structured viruses characterised recently and belong to two separate genogroups. The capsid genes of these viruses were expressed in insect cells using recombinant baculoviruses. Both SV (genogroup 1) and LV (genogroup 2) capsid proteins self-assembled to form virus-like particles (VLPs). The VLPs were used in a standard enzyme-linked immunosorbent assay (ELISA) to screen for antibodies to SV and LV in 1,729 age-stratified human sera collected in Verona, Italy between January and November 1996. SV VLPs were labile compared with LV VLPs. There was a large difference in the prevalence of SV (28.7%) compared with LV (91.2%). However, presentation of SV VLPs using chicken egg yolk antibody-coated wells (IgY capture ELISA) with a subset of serum samples from patients (0-19 years) increased the number of positive sera significantly (50.5%), indicating that SV antigen integrity is an important factor in the assay. Recent reverse transcription-polymerase chain reaction (RT-PCR) studies have shown that LV is circulating currently and analysis of IgY capture ELISA data showed greater reactivity for LV than SV, reflecting a genuinely lower rate of recent infection by this genogroup 1 virus.
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Affiliation(s)
- E Pelosi
- Istituto di Microbiologia, Universita di Verona, Italy
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19
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Liu BL, Viljoen GJ, Clarke IN, Lambden PR. Identification of further proteolytic cleavage sites in the Southampton calicivirus polyprotein by expression of the viral protease in E. coli. J Gen Virol 1999; 80 ( Pt 2):291-296. [PMID: 10073687 DOI: 10.1099/0022-1317-80-2-291] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Southampton virus (SV) is a human enteric calicivirus with a positive-sense RNA genome which encodes a protease as part of a large precursor polyprotein. Expression vectors based on pRSET were constructed carrying the entire 3C-like viral protease (3Cpro) sequence together with flanking sequences from a region of the viral genome 3'-distal to the putative helicase-encoding region. Expression from these vectors in E. coli resulted in discrete protein products with smaller than expected molecular sizes. This confirmed that an active viral protease was produced in E. coli and that the protease was capable of cleaving the expressed protein at defined sites. Expressed cleavage products surrounding the protease region of the viral polyprotein were separated by SDS-PAGE, transferred to PVDF membranes and subjected to N-terminal sequence analysis. Cleavage occurred at an EG dipeptide at the N terminus of the putative VPg (961E/GKNKG) and also at the protease/polymerase boundary (1280E/GGDKG). The N terminus of the protease was released from the VPg C terminus at an EA dipeptide in the sequence 1099E/APPTL. These studies demonstrate that SV enteric calicivirus encodes a 3C-like protease with a specificity similar to the picornaviral 3C protease and that the SV polyprotein is cleaved into at least six mature products.
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20
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Liu BL, Lambden PR, Günther H, Otto P, Elschner M, Clarke IN. Molecular characterization of a bovine enteric calicivirus: relationship to the Norwalk-like viruses. J Virol 1999; 73:819-25. [PMID: 9847396 PMCID: PMC103897 DOI: 10.1128/jvi.73.1.819-825.1999] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Jena virus (JV) is a noncultivatable bovine enteric calicivirus associated with diarrhea in calves and was first described in Jena, Germany. The virus was serially passaged 11 times in colostrum-deprived newborn calves and caused diarrheal disease symptoms at each passage. The complete JV genome sequence was determined by using cDNA made from partially purified virus obtained from a single stool sample. JV has a positive-sense single-stranded RNA genome which is 7,338 nucleotides in length, excluding the poly(A) tail. JV genome organization is similar to that of the human Norwalk-like viruses (NLVs), with three separate open reading frames (ORFs) and a 24-nucleotide sequence motif located at the 5' terminus of the genome and at the start of ORF 2. The polyprotein (ORF 1) consists of 1,680 amino acids and has the characteristic 2C helicase, 3C protease, and 3D RNA polymerase motifs also found in the NLVs. However, comparison of the N-terminal 100 amino acids of the JV polyprotein with those of the group 1 and group 2 NLVs showed a considerable divergence in sequence. The capsid protein (ORF 2) at 519 amino acids is smaller than that of all other caliciviruses. JV ORF 2 was translated in vitro to produce a 55-kDa protein that reacted with postinfection serum but not preinfection serum. Phylogenetic studies based on partial RNA polymerase sequences indicate that within the Caliciviridae JV is most closely related to the group 1 NLVs.
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Affiliation(s)
- B L Liu
- Molecular Microbiology Group, University Medical School, Southampton General Hospital, Southampton SO16 6YD, United Kingdom
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21
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James VL, Lambden PR, Caul EO, Clarke IN. Enzyme-linked immunosorbent assay based on recombinant human group C rotavirus inner capsid protein (VP6) To detect human group C rotaviruses in fecal samples. J Clin Microbiol 1998; 36:3178-81. [PMID: 9774561 PMCID: PMC105297 DOI: 10.1128/jcm.36.11.3178-3181.1998] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/1998] [Accepted: 08/18/1998] [Indexed: 11/20/2022] Open
Abstract
A recent study showed that 43% of a population in the United Kingdom were seropositive for group C rotavirus. The higher than expected incidence may be due to limited diagnosis of acute human group C rotavirus infections because no routine test is available. Human group C rotavirus infections are routinely diagnosed by electron microscopy (EM) and a negative group A rotavirus enzyme-linked immunosorbent assay (ELISA) result. An antigen-detection ELISA was developed with hyperimmune antibodies raised to human group C rotavirus recombinant VP6 (Bristol strain) expressed in insect cells. The assay was used to screen fecal samples to determine the prevalence of group C rotavirus infection. Samples positive by ELISA were confirmed by EM, polyacrylamide gel electrophoresis of double-stranded RNA, or detection of the VP6 gene by reverse transcription-PCR. Retrospective analysis indicated a 1 to 2% detection rate of positivity among samples from patients with acute diarrhea.
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Affiliation(s)
- V L James
- Public Health Laboratory, Southampton General Hospital, Southampton SO16 6YD, United Kingdom.
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22
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Abstract
Caliciviruses are important veterinary and human pathogens. The viruses gain their name from characteristic cup-shaped structures seen on the virion surface by negative stain electron microscopy. In humans caliciviruses are a major cause of diarrhoeal disease. There are two fundamentally different genome structures amongst human caliciviruses. The Norwalk-like or small round structured viruses (SRSVs) are viruses that have an amorphous structure when viewed by EM, they have a genome composed of 3 major open reading frames (ORFs). These viruses cause epidemic gastroenteritis amongst all age groups. In contrast, the 'classic' human caliciviruses (HuCVs) display the typical calicivirus surface structure and have their capsid ORF fused to and contiguous with the non structural proteins forming one giant polyprotein. HuCVs are predominantly associated with paediatric infections and are only a minor cause of disease in humans. Spread of disease for both SRSVs and HuCVs is usually by faecal oral transmission. SRSVs are a major cause of foodborne gastroenteritis especially linked to the consumption of sewage-contaminated shellfish. However, there is no evidence that these viruses replicate in shellfish or that they originate from an animal source.
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Affiliation(s)
- I N Clarke
- Molecular Microbiology Group, University Medical School, Southampton General Hospital, U.K
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23
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Abstract
An enteric calicivirus showing the classic cup-shaped surface morphology was identified in a stool sample obtained from a child with symptoms of acute gastroenteritis (Portishead virus, PHV). Genomic RNA was extracted directly from the PHV stool sample and amplified by RT-PCR using primers based on the Manchester isolate of HuCV. The 3' terminus of the cDNA was defined by homopolymer tailing with dATP and revealed an additional 165 nucleotides suggesting that the previously determined Manchester HuCV (MV) genome sequence was incomplete. Homopolymer tailing of MV cDNA primed using sequence data from the 5' terminus of PHV allowed extension of the MV genome by a further 165 nucleotides thereby increasing the overall genome length to 7431 nucleotides and resulting in an additional 72 amino acids at the N-terminus of the polyprotein. A conserved sequence motif typical of other caliciviruses was also identified at the extreme 5'-terminus of the genome.
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Affiliation(s)
- B Liu
- Molecular Microbiology, University Medical School, Southampton General Hospital, UK
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24
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Noel JS, Liu BL, Humphrey CD, Rodriguez EM, Lambden PR, Clarke IN, Dwyer DM, Ando T, Glass RI, Monroe SS. Parkville virus: a novel genetic variant of human calicivirus in the Sapporo virus clade, associated with an outbreak of gastroenteritis in adults. J Med Virol 1997; 52:173-8. [PMID: 9179765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This report describes the characterization of Parkville virus, the etiologic agent of an outbreak of foodborne gastroenteritis, that has the morphology of a calicivirus and genetic properties that distinguish it from previously identified strains in the Sapporo/Manchester virus clade. Sequence analysis of the Parkville virus genome showed it contained the RNA-dependent RNA polymerase motifs GLPSG and YGDD characteristic of members of the family Caliciviridae with an organization identical to that reported for the Manchester virus where the capsid region of the polyprotein is fused to the RNA polymerase. Parkville virus however, demonstrates considerable sequence divergence from both the Manchester and Sapporo caliciviruses, providing the first indications that genetic diversity exists within caliciviruses of this previously homogeneous clade. On the basis of recent advances in the genetic characterization of members of the family Caliciviridae, we propose a new interim phylogenetic classification system in which Parkville virus would be included with Manchester and Sapporo virus as a separate group distinct from the small round-structured viruses (Norwalk-like viruses) that also cause diarrhea in humans.
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Affiliation(s)
- J S Noel
- Viral Gastroenteritis Unit, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
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25
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Noel JS, Liu BL, Humphrey CD, Rodriguez EM, Lambden PR, Clarke IN, Dwyer DM, Ando T, Glass RI, Monroe SS. Parkville virus: A novel genetic variant of human calicivirus in the Sapporo virus clade, associated with an outbreak of gastroenteritis in adults. J Med Virol 1997. [DOI: 10.1002/(sici)1096-9071(199706)52:2<173::aid-jmv10>3.0.co;2-m] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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26
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Abstract
Chlamydiae exhibit low interspecies DNA homology and plasmids from different chlamydial species can be readily distinguished by Southern blot analysis and restriction enzyme profiling. In contrast, available plasmid sequence data from within the species Chlamydia trachomatis indicate that plasmids from human isolates are highly conserved. To evaluate the nature and extent of plasmid variation, the complete nucleotide sequences were determined for novel plasmids from three diverse non-human chlamydial isolates: pCpA1 from avian Chlamydia psittaci (N352); pCpnE1 from equine Chlamydia pneumoniae (N16); and pMoPn from C. trachomatis mouse pneumonitis. Comparison of the sequence data did not identify an overall biological function for the plasmid but did reveal considerable sequence conservation (> 60%) and a remarkably consistent genomic arrangement comprising eight major ORFs and four 22 bp tandem repeats. The plasmid sequences were close to 7500 nucleotides in length (pCpA1, 7553 bp; pMoPn, 7502 bp) however the equine C. pneumoniae plasmid was smaller (7362 bp) than all other chlamydial plasmids. The reduced size of this plasmid was due to a single large deletion occurring within ORF 1; this potentially generates two smaller ORFs. The disruption of ORF 1 is the only significant variation identified amongst the chlamydial plasmids and could prove important for future vector development studies.
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Affiliation(s)
- N S Thomas
- Molecular Microbiology, University of Southampton Medical School, Southampton General Hospital, Southampton S016 6YD, UK
| | - M Lusher
- University of Manchester, Department of Pathological Sciences, Virology Division, Oxford Road, Manchester M13 9PT, UK
| | - C C Storey
- University of Manchester, Department of Pathological Sciences, Virology Division, Oxford Road, Manchester M13 9PT, UK
| | - I N Clarke
- Molecular Microbiology, University of Southampton Medical School, Southampton General Hospital, Southampton S016 6YD, UK
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27
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Green SM, Lambden PR, Caul EO, Clarke IN. Capsid sequence diversity in small round structured viruses from recent UK outbreaks of gastroenteritis. J Med Virol 1997; 52:14-9. [PMID: 9131452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Genetic typing of small round structured viruses (SRSVs) by reverse transcription-polymerase chain reaction (RT-PCR) and sequencing has been confined to analysis of the RNA polymerase because of the considerable genome variability outside of this region. To provide capsid sequence data for epidemiological studies and outbreak investigations, a broadly reactive capsid PCR was developed using two sets of degenerate, inosine-containing primers. Primer pairs Capla/Caplb and Caplla/Capllb specifically amplify a 223-bp region of the SRSV capsid open reading frame from SRSV genetic groups I and II, respectively. The capsid PCR was used to investigate SRSVs from nine UK outbreaks of gastroenteritis occurring between 1992 and 1995. Differential amplification by the primer pairs suggested that three strains belonged to genetic group I and six to genetic group II. The capsid amino acid sequences of the group I strains were 75.9% to 79.3% identical with Sot/91/UK (group I), while those of the group II strains were 75.9% to 98.3% identical with Bri/93/UK (group II). Phylogenetic comparison of the capsid region from the outbreak strains and 13 previously characterised SRSVs revealed clusters of strains closely related to Bri/93/UK and Tor/77/C within genetic group II. With the exception of some Bri/93/UK-like strains, there was no correlation between capsid sequence and the geographical origin of SRSVs. UK strains were found with greater than 90% capsid sequence identity to SRSVs from various locations worldwide including Australia (Cam/94/A), Canada (Tor/77/C), Hawaii (Haw/71/US), and Saudi Arabia (DSV395/90/SA) together with group I (B447/92/UK) and group II (Yat/94/UK) strains that were genetically distinct from known SRSV capsids. Three SRSVs very closely related to Bri/93/UK were from recent UK hospital outbreaks. These Bri/93/UK-like strains appear to be prevalent in the UK.
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Affiliation(s)
- S M Green
- Public Health Laboratory, University Medical School, Southampton General Hospital, UK
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28
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Abstract
The gene coding for the major inner capsid protein VP6 of human group C rotavirus was cloned into baculovirus using the pBlueBac2 vector and expressed in insect cells. When cultured in High Five cells, VP6 was expressed at a high level and exported to the cell culture medium. Purified VP6 was used to immunise rabbits. Hyperimmune rabbit serum, which reacted with native human group C rotavirus in infected cells, was used to develop and optimise an EIA for the detection of antibodies to group C rotavirus using the recombinant VP6 as a source of antigen. In a local epidemiological survey of 1000 sera grouped by age, an average of 43% of samples were found to have antibodies to human group C rotavirus with the highest proportion (66%) in the 71-75 year age group. In comparison, 97% of adults and 85% of children had antibodies to recombinant VP6 from the bovine RF strain of group A rotavirus. These results suggest that infection with human group C rotavirus is a common occurrence despite the apparent rarity of reports of human group C rotavirus in clinical samples from patients with gastroenteritis.
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Affiliation(s)
- V L James
- Public Health Laboratory, Southampton General Hospital, UK
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29
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Affiliation(s)
- I N Clarke
- Molecular Microbiology Group, University Medical School, Southampton General Hospital, UK.
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30
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Abstract
An immunogenic loop within the diphtheria toxin has been deleted from the B-subunit by a modification of the inverse polymerase chain reaction (IPCR) and replaced by a unique restriction endonuclease site. An oligonucleotide encoding an identified epitope sequence from the major outer membrane protein of Neisseria meningitidis of similar size and structure to that deleted has been introduced into the restriction site. Expression of the resulting chimeric B-subunit from Escherichia coli yielded a protein that was recognised by a panel of antibodies specific for the meningococcal epitope. Initial immunisation data suggest that this protein could elicit an antibody response against both diphtheria toxin and meningococcal proteins.
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Affiliation(s)
- N Johnson
- University Department of Molecular Microbiology, Southampton General Hospital, UK
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31
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Ward SJ, Scopes D, Christodoulides M, Clarke IN, Heckels JE. Expression of Neisseria meningitidis class 1 porin as a fusion protein in Escherichia coli: the influence of liposomes and adjuvants on the production of a bactericidal immune response. Microb Pathog 1996; 21:499-512. [PMID: 8971689 DOI: 10.1006/mpat.1996.0079] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
High level expression of meningococcal class 1 protein was achieved in Escherichia coli using the p-GEMEX-1 vector, in which the protein was expressed in inclusion bodies (IB), as a fusion with the bacteriophage T7 gene 10 capsid protein. The fusion protein (FP) was engineered with a factor Xa protease site between the gene 10 and class 1 protein, but treatment with the enzyme resulted in cleavage at additional sites within the class 1 protein. Since it was not possible to remove the leader protein, the intact FP provided an alternative antigen for immunization. Antisera raised to FP, solubilized from IB and incorporated into liposomes, generated a subtype-specific response which was weakly bactericidal for meningococci. In order to remove any possible effect of E. coli LPS present in IB, the FP was further purified by SDS-PAGE and incorporated into liposomes, either alone or in combination with the adjuvants monophosphoryl lipid A or muramyl dipeptide. The incorporation of adjuvants in liposomes resulted in stimulation of the overall immune response to FP, but the resulting antisera were not bactericidal. However an effective bactericidal response was obtained with the purest preparation of FP in liposomes, without any additional adjuvants, revealing that attempts to increase further the immunogenicity of such antigens must not be at the expense of interfering with optimal protein folding.
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Affiliation(s)
- S J Ward
- Molecular Microbiology Group, University of Southampton Medical School, Southampton General Hospital, U.K
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32
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Abstract
A genomic clone of the small, round-structured virus Southampton virus (SV) was constructed from a set of overlapping PCR amplicons. Sequence analysis confirmed the absence of mutations and accurate ligation of the PCR products. The SV cDNA was cloned into a vector for in vitro production of RNA and subsequent translation by rabbit reticulocyte lysate. Two polypeptides corresponding to the N-terminal and C-terminal regions of the viral polyprotein were expressed in Escherichia coli and used to produce murine antisera for detection of translation products. Three major translation products of 113, 48, and 41 kDa were identified in a coupled transcription-translation system. The large 113-kDa protein reacted with antisera raised against the C-terminal region of the polyprotein and represents a precursor of the viral RNA polymerase. The 48-kDa protein detected in vitro reacted specifically with antisera raised against the polyprotein N terminus, showing that translation was initiated in SV at the three tandem in-frame AUG codons at the 5' end of the genome. A series of nested 3' deletions of the large open reading frame encoding the viral polyprotein was used to define the translation initiation site and genomic location of the viral protease. The results are consistent with a model in which translation of the viral genome is initiated at one of the three in-frame AUG codons starting at nucleotide position 5 and in which active viral protease is produced following translation of a region located between NheI (nucleotide 3052) and SphI (nucleotide 4056), resulting in rapid cleavage of a large precursor protein. Abolition of the viral 3C-like protease activity by site-directed mutagenesis of the putative active-site cysteine (Cys-1238) resulted in production of a large protein of approximately 200 kDa which reacted with both N-terminal and C-terminal antisera. Two potential polyprotein cleavage sites containing the preferred picornaviral QG recognition site were identified on either side of the putative 2C-like helicase region of the polyprotein. Proteolysis at these positions would give rise to products with relative molecular masses identical to those of the products detected in the rabbit reticulocyte system. Site-directed mutagenesis was used to introduce a single base change which resulted in the substitution of glutamine residues with proline residues at amino acids 399 and 762. These mutations completely abolished cleavage of the polyprotein at these positions and gave rise to alternative products with molecular masses which matched the predicted sizes for a single cleavage at either Q-399 or Q-762. These data indicate that the small, round-structured virus Southampton virus produces a 3C-like protease which has two primary cleavage sites at positions 399 and 762. Proteolytic cleavage at these positions releases the putative viral 2C-like helicase.
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Affiliation(s)
- B Liu
- Molecular Microbiology Group, University Medical School, Southampton General Hospital, Southampton, United Kingdom
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33
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Abstract
The complete nucleotide sequence of genome segment 4 from the human group C rotavirus (Bristol strain) was determined. Comparison of the nucleotide sequences of the genome termini with the consensus 5' and 3' terminal non-coding sequences of the human group C rotavirus genome revealed characteristic 5' and 3' sequence motifs. Human group C rotavirus genome segment 4 is 2,166bp long and encodes a single open reading frame of 2,082 nucleotides (693 amino acids) starting at nucleotide 55 and terminating at nucleotide 2,136 giving a 3' untranslated region of 30 nucleotides. Alignment with the porcine group C VP3 equivalent gene showed the human gene is one amino acid longer, and that the proteins have 84.1% amino acid sequence identity. A conserved potential nucleotide binding motif shared with the porcine VP3 sequence was identified. Analogy with the group A rotaviruses suggested that the genome segment 4 encodes the group C rotavirus guanylyltransferase.
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34
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Abstract
The complete nucleotide sequence of genome segment 11 from the noncultivatable, human group C rotavirus (Bristol strain) was determined. Comparison of the nucleotide sequence of the segment termini with the consensus 5' and 3' terminal noncoding sequences of the human group C rotavirus genome revealed characteristic 5' and 3' sequences. Human group C rotavirus genome segment 11 is 613 bp long and encodes a single open reading frame of 450 nucleotides (150 amino acids) starting at nucleotide 39 and terminating at nucleotide 489, leaving a long 3' untranslated region of 124 nucleotides. The predicted translation product has a calculated molecular weight of 17.7 kD and contains four potential N-linked glycosylation sites. No significant homologies to other viral proteins were found in database searches. Hydropathy analysis predicted the human group C rotavirus genome segment 11 translation product has a hydrophilic carboxy terminus (amino acids 54-150) and a hydrophobic amino terminus (amino acids 1-53) that can be further subdivided into three short hydrophobic sequences--H1, H2, and H3. These features are analogous to the integral membrane glycoprotein NSP4 encoded by group A rotavirus gene 10.
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Affiliation(s)
- Y Deng
- University Medical School, Southampton General Hospital, United Kingdom
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35
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Abstract
One of the critical developmental events during the unique intracellular life cycle of Chlamydiae is their differentiation from a metabolically active, replicative form or reticulate body (RB) to an infectious extracellular form of the organism (elementary body or EB). This process is characterized by the expression of two extraordinarily cysteine-rich envelope proteins of molecular masses 9 kDa and 60 kDa. We describe the molecular cloning and sequence determination of the 9 kDa cysteine-rich proteins (CrPs) of C. pneumoniae and C. psittaci. Comparison of these 9 kDa CrP amino acid sequences with those of C. trachomatis showed regions of structural variation and conservation. Transcription of the 9 kDa CrP genes occurred as both a monocistronic message and as a bicistronic message which included the 60 kDa CrP gene. Transcription of the 9 kDa and 60 kDa CrP genes was tightly linked to the chlamydial growth cycle with synthesis of their mRNAs and consequent translation of the 60 kDa CrPs occurring as RBs differentiated to form EBs. The maximal rate of transcription occurred late in the growth cycle from a single but highly conserved promoter which had close similarity with the Escherichia coli consensus promoter sequences. A stem and loop structure which could be involved in regulating translation of mRNA occurred in all three species between the transcriptional start point and the ribosome binding site. Although transcription is initiated from a single promoter in all three chlamydial species, transcriptional termination points for the monocistronic and bicistronic mRNAs differ in both number and position.
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Affiliation(s)
- M W Watson
- University Medical School, Southampton General Hospital, UK
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36
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Dingle KE, Lambden PR, Caul EO, Clarke IN. Human enteric Caliciviridae: the complete genome sequence and expression of virus-like particles from a genetic group II small round structured virus. J Gen Virol 1995; 76 ( Pt 9):2349-55. [PMID: 7561776 DOI: 10.1099/0022-1317-76-9-2349] [Citation(s) in RCA: 126] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Comparisons of the RNA polymerase and capsid sequences of small round structured viruses (SRSVs) have recently shown these are genetically diverse viruses which fall into two distinct groups. The genomes of two group I viruses, Southampton and Norwalk viruses have been characterized; however, similar data for the genetic group II SRSVs have not been available until now. We report here the complete genome sequence of a recent group II SRSV, Lordsdale virus. The Lordsdale virus genome is 7555 nt in length and has a similar organization to the group I SRSVs. The large ORF in the 5' half of the genome (5100 nt) is shorter than the group I SRSV ORF1 (5367 nt), but has the characteristic 2C helicase, 3C protease and 3D RNA polymerase enzyme motifs. ORF2, encoding the structural protein is of a similar size to the group I viruses but the small 3'-terminal ORF is significantly larger in group II. A highly conserved sequence of 28 nt was identified at the start of Lordsdale virus ORF1 and repeated at the start of ORF2. These conserved motifs are typical of the animal caliciviruses. Comparison of the 150 N-terminal amino acids in the ORF1 protein revealed little identity between the two SRSV genetic groups, reflecting the shorter ORF1 in the group II virus. Recombinant baculoviruses containing ORF2 and ORF3 sequences were constructed and used to express large quantities of the group II Lordsdale virus structural protein. The capsid protein formed virus-like particles by self assembly which resembled 'empty' SRSVs.
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Affiliation(s)
- K E Dingle
- Department of Molecular Microbiology, University Medical School, Southampton General Hospital, UK
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37
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Liu BL, Clarke IN, Caul EO, Lambden PR. Human enteric caliciviruses have a unique genome structure and are distinct from the Norwalk-like viruses. Arch Virol 1995; 140:1345-56. [PMID: 7661689 DOI: 10.1007/bf01322662] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Classic human enteric caliciviruses (HuCVs) have a distinctive morphology and are primarily associated with pediatric acute gastroenteritis. Although morphologically distinct from the small round structured viruses (SRSVs), the classic HuCVs are thought to be closely related and were anticipated to have a similar genome organisation. We report the first genome sequence and molecular characterisation of a classic human enteric calicivirus associated with a case of acute vomiting and diarrhoea in an infant. The RNA genome (7266 nt) is smaller than the genome of SRSVs from the two genetic groups and has a unique arrangement of open reading frames. Further analysis of the 3' terminal 3 kb from a second unrelated isolate confirmed this genomic organisation. Analysis of capsid and RNA polymerase sequences together with the unique genomic organisation of classic HuCV suggest these viruses are more closely related to the animal caliciviruses than the enteric SRSV group of viruses.
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Affiliation(s)
- B L Liu
- Molecular Microbiology Group, University Medical School, Southampton General Hospital, U.K
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38
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Green SM, Lambden PR, Caul EO, Ashley CR, Clarke IN. Capsid diversity in small round-structured viruses: molecular characterization of an antigenically distinct human enteric calicivirus. Virus Res 1995; 37:271-83. [PMID: 8533462 DOI: 10.1016/0168-1702(95)00041-n] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Studies of antigenic variation between small round-structured viruses (SRSVs) using immune electron microscopy have revealed 3 antigenic types currently circulating in the UK represented by the strains SRSV/Bri/93/UK, SRSV/Sot/91/UK and SRSV/Mel/89/UK. Mel/89/UK RNA was isolated from a 1989 school outbreak of gastroenteritis. The 3'-terminal 3435 nucleotides (excluding the poly(A) tail) were determined by RT-PCR and cDNA sequencing, completing our molecular characterization of antigenically diverse SRSVs. Coding regions for the calicivirus RNA polymerase and capsid protein were found together with a 3' open reading frame of unknown function. The polymerase region was most highly conserved between Mel/89/UK and the other two SRSVs while the 3' open reading frame exhibited extreme variation. Phylogenetic analysis of SRSV capsids showed that Mel/89/UK differed significantly from Bri/93/UK and Sot/91/UK (62 and 39% identity, respectively) and was distinct from 6 other non-UK SRSVs that had been previously characterized. This was consistent with the designation of Mel/89/UK as a novel antigenic variant. Comparison of the capsid amino acid sequences of the 3 UK strains together with the antigenically distinct SRSV/Nor/68/US revealed a hypervariable region that could be surface-exposed and contain the SRSV antigenic determinants.
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Affiliation(s)
- S M Green
- Department of Molecular Microbiology, University Medical School, Southampton General Hospital, UK
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39
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Abstract
Caliciviruses cause a wide spectrum of important diseases. These viruses have a positive-sense single-stranded RNA genome; recently, the complete genome sequences of several caliciviruses have been determined. This review outlines the genome organization and phylogenetic relationships of the animal and candidate human caliciviruses.
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Affiliation(s)
- P R Lambden
- Molecular Microbiology Group, University of Southampton Medical School, Southampton General Hospital, UK
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40
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Lambden PR, Liu B, Clarke IN. A conserved sequence motif at the 5' terminus of the Southampton virus genome is characteristic of the Caliciviridae. Virus Genes 1995; 10:149-52. [PMID: 8560774 DOI: 10.1007/bf01702595] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We have determined the 5'terminal cDNA sequence for the genome of Southampton virus, a recently characterized, human, small round-structured virus (SRSV). Genomic RNA was extracted directly from a stool sample and amplified by RT-PCR by homopolymer tailing of the 3' terminus of the cDNA. The additional sequence increases the overall length of the Southampton virus genome by 12 nucleotides, resulting in a significant change to the genome organization by extending the first large open reading frame (ORF) by 51 amino acids. The 5'terminal bases pGpT and the presence of conserved genome and putative subgenomic RNA terminal motifs are now prominent features shared between the human SRSV Southampton virus and the animal caliciviruses rabbit hemorrhagic disease virus and feline calicivirus.
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Affiliation(s)
- P R Lambden
- University Medical School, Southampton General Hospital, UK
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41
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Green SM, Lambden PR, Deng Y, Lowes JA, Lineham S, Bushell J, Rogers J, Caul EO, Ashley CR, Clarke IN. Polymerase chain reaction detection of small round-structured viruses from two related hospital outbreaks of gastroenteritis using inosine-containing primers. J Med Virol 1995; 45:197-202. [PMID: 7775939 DOI: 10.1002/jmv.1890450215] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Two outbreaks of gastroenteritis in the UK which occurred nine days apart at Lymington and Southampton hospitals were investigated. The clinical and epidemiological features of both outbreaks were characteristic of small round-structured virus (SRSV) infection with rapid onset of diarrhoea and/or nausea and vomiting and propagation of the outbreaks by secondary spread. SRSV particles were observed by immune electron microscopy (EM) in 60% of faecal samples from both outbreaks and no other pathogens were detected. The index case for the second outbreak was a patient who was admitted with diarrhoea and vomiting after being discharged from Lymington hospital during the first outbreak. The possibility that the two outbreaks were caused by the same strain of SRSV was investigated by the polymerase chain reaction (PCR). New inosine-containing PCR primers were designed to amplify the RNA polymerase region of SRSV cDNA from genetic groups I and II. The PCR using the group II primers achieved a higher detection rate for SRSVs in faecal samples (68% of samples positive from both outbreaks) than immune EM. SRSVs were not detected using the group I primers or using conventional degenerate PCR primers. The nucleotide sequences of PCR amplicons from both outbreaks were identical providing molecular epidemiological evidence for the involvement of a single SRSV strain. Comparison of the RNA polymerase region of this virus with the equivalent regions of genetic group I (69.4-75.0% amino acid identify) and genetic group II (88.9-100% amino acid and 77.1-88.1% nucleotide identity) SRSVs revealed that the causative SRSV was a distinct member of genetic group II.
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Affiliation(s)
- S M Green
- Department of Molecular Microbiology, University Medical School, Southampton General Hospital, United Kingdom
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42
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Abstract
Several outbreaks of Group C rotavirus infection have occurred in the United Kingdom, in one instance infection was associated with the death of a 4-month-old infant in the Bristol area. The origin of human group C rotavirus is unknown although there has been some speculation that porcine species may be a possible source of human infection. Direct reverse transcription-polymerase chain reaction sequencing of VP7 genes from two UK outbreaks (Bristol and Preston) and sequence analysis from a sporadic case of infection from Brazil (Belém) showed that each of these genes was identical in size (1,063 bp) and has revealed a surprising level (97.8-99.8%) of gene sequence conservation. Sequence comparisons with an isolate from Japan imply that the human group C rotaviruses so far characterised originate from a recent common ancestor with a worldwide distribution.
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Affiliation(s)
- A S Grice
- Department of Molecular Microbiology, University Medical School, Southampton General Hospital, United Kingdom
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43
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Abstract
A cDNA copy of the third genomic RNA segment of a noncultivatable human group C rotavirus (Bristol) was generated by single primer amplification. Human group C rotavirus genome segment 3 contains 2283 bp and encodes the VP4 gene with an open reading frame of 2232 nucleotides (744 amino acids) starting at nucleotide 21 and terminating at nucleotide 2251. PCR primers designed from the 5' and 3' terminal sequences of the C/Bristol VP4 gene were used to amplify the corresponding VP4 gene of a human group C rotavirus from Belém, Brazil. Nucleotide sequence comparisons of the Bristol and Belém VP4 genes revealed 45 differences of which only 6 were predicted to give amino acid changes. Alignment of the two human VP4 sequences with the prototype porcine group C/Cowden rotavirus VP4 showed only 71.2% nucleotide sequence identity. Protein sequence alignments showed that the human group C rotavirus VP4 sequences were 8 amino acids longer than the porcine VP4 sequence with an insertion of 6 amino acids, 252NSKLGD257 adjacent to the proposed proteolytic cleavage region (amino acids 231-250). The large overall number of differences between the human and porcine VP4 sequences strongly suggested that the porcine C/Cowden isolate may belong to a different group C rotavirus P "serotype." In contrast the very close similarity of the VP4 sequences of the UK and Brazilian group C rotaviruses support the hypothesis that these human isolates originate from a recent common ancestor.
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Affiliation(s)
- P A Fielding
- Department of Molecular Microbiology, University Medical School, Southampton General Hospital, United Kingdom
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44
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Green SM, Dingle KE, Lambden PR, Caul EO, Ashley CR, Clarke IN. Human enteric Caliciviridae: a new prevalent small round-structured virus group defined by RNA-dependent RNA polymerase and capsid diversity. J Gen Virol 1994; 75 ( Pt 8):1883-8. [PMID: 8046390 DOI: 10.1099/0022-1317-75-8-1883] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Sequence comparison of the RNA-dependent RNA polymerases of small round-structured viruses (SRSVs) from 10 recent U.K. outbreaks of gastroenteritis revealed significant genetic variation. Computer analyses indicated that these viruses can be divided into two discrete groups. SRSV group I contains the previously characterized antigenic type 1 Norwalk and type 3 Southampton viruses. The amino acid sequences of the RNA polymerase, capsid and ORF3 of these two viruses are relatively similar (about 92%, 69% and 72% amino acid identity, respectively). A representative member of group II SRSVs, Bristol virus, was subjected to a detailed genetic analysis. Bristol virus is a recent antigenic type 2 isolate from a U.K. hospital outbreak of gastroenteritis. Using a single clinical sample the 3'-terminal 3881 nucleotide cDNA sequence [excluding the poly(A) tail] of this virus was determined. Analysis of the sequence revealed significant differences from those of group I viruses with the RNA polymerase region, capsid and ORF3 showing only about 62%, 43% and 30% amino acid identity respectively with the equivalent proteins of the Norwalk and Southampton viruses. These data suggest that the morphologically identical SRSVs belong to at least two genetically distinct groups.
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Affiliation(s)
- S M Green
- Department of Molecular Microbiology, University Medical School, Southampton General Hospital, U.K
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45
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Watson MW, Lambden PR, Everson JS, Clarke IN. Immunoreactivity of the 60 kDa cysteine-rich proteins of Chlamydia trachomatis, Chlamydia psittaci and Chlamydia pneumoniae expressed in Escherichia coli. Microbiology (Reading) 1994; 140 ( Pt 8):2003-11. [PMID: 7522846 DOI: 10.1099/13500872-140-8-2003] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The 60 kDa cysteine-rich proteins (CrPs) of Chlamydia are developmentally regulated outer envelope proteins synthesized late in the chlamydial growth cycle. These proteins, found only on the extracellular infectious elementary bodies, elicit major antibody responses in chlamydial infection. We have cloned and expressed in Escherichia coli the complete 60 kDa CrP genes from Chlamydia trachomatis, C. psittaci and C. pneumoniae. The recombinant products were expressed as either 'native' proteins or as fusions with the bacteriophage T7 gene 10 protein. Electron microscopy showed that recombinant proteins were produced as insoluble inclusions within the E. coli host cells. The recombinant 60 kDa CrPs were purified and used to raise high titre polyclonal antisera. In immunoblot analysis these antisera reacted with the 60 kDa CrPs from purified elementary bodies of all three chlamydial species in a genus-specific manner. Further molecular analysis allowed the genus-specific cross-reacting epitopes to be localized by using overlapping synthetic peptides covering the C. trachomatis 60 kDa CrP. Immunogold labelling experiments, using purified infectious elementary bodies from the three chlamydial species indicated that the 60 kDa CrPs are not surface accessible to antibody binding.
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Affiliation(s)
- M W Watson
- Faculty of Medicine, Southampton General Hospital, UK
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46
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47
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Abstract
Small round-structured viruses (SRSVs), also known as Norwalk or Norwalk-like viruses, are the major worldwide cause of acute, epidemic nonbacterial gastroenteritis in humans. These viruses, which contain a single-stranded RNA genome, have remained refractory to molecular characterization because of the small amounts of virus in clinical samples and the absence of an animal model and an in vitro culture system. The complete genomic nucleotide sequence of an SRSV, Southampton virus, was determined. The 7696-nucleotide RNA genome encodes three open reading frames whose sequences and organization strongly support proposals that SRVSs are members of the Caliciviridae.
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Affiliation(s)
- P R Lambden
- Department of Molecular Microbiology, University Medical School, Southampton General Hospital, United Kingdom
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48
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Hayes LJ, Bailey RL, Mabey DC, Clarke IN, Pickett MA, Watt PJ, Ward ME. Genotyping of Chlamydia trachomatis from a trachoma-endemic village in the Gambia by a nested polymerase chain reaction: identification of strain variants. J Infect Dis 1992; 166:1173-7. [PMID: 1402030 DOI: 10.1093/infdis/166.5.1173] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Direct amplification of the major outer membrane protein (MOMP) gene by polymerase chain reaction (PCR) was used to identify Chlamydia trachomatis in eye swabs from clinically active cases of endemic trachoma in a Gambian village. Chlamydial DNA was detected in 51% of 96 subjects with clinically active disease and in 5% of 37 clinically negative individuals. The PCR detection was combined with typing, using nested primers to variable sequences (VS) 1, 2, and 4 of the MOMP genes to distinguish between trachoma genotypes A, B, and C, respectively. Genotypes A and B were detected in the village, with some individuals harboring both genotypes within the same eye. DNA sequencing revealed strain variants of both genotypes. Typing of genotype and strain variants is now in progress to study trachoma transmission within the village.
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Affiliation(s)
- L J Hayes
- University Department of Microbiology, Southampton General Hospital, United Kingdom
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49
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Cooke SJ, Clarke IN, Freitas RB, Gabbay YB, Lambden PR. The correct sequence of the porcine group C/Cowden rotavirus major inner capsid protein shows close homology with human isolates from Brazil and the U.K. Virology 1992; 190:531-7. [PMID: 1326817 DOI: 10.1016/0042-6822(92)91248-s] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Amino acid sequence alignments between the human group C/Bristol and the published porcine group C/Cowden VP6 proteins have revealed a region of extreme sequence divergence. We have been unable to confirm the nucleotide sequence of the Cowden VP6 gene corresponding to this region of divergence. Direct sequencing of a PCR-amplified cDNA pool has revealed a frame shift, and three nucleotide changes, within the published sequence of the porcine (Cowden) VP6 gene. The corrected sequence of the porcine protein revealed a closer homology with VP6 from the Bristol strain and two new human group C rotavirus isolates. Atypical rotaviruses have been detected in the feces of children living in Belém, Brazil, and Preston, U.K. Direct sequencing of PCR-amplified cDNA corresponding to the VP6 gene of one isolate from each location confirmed the presence of a group C rotavirus. The complete nucleotide sequences of the VP6 genes from the group C/Belém and C/Preston rotaviruses contained an open reading frame of 1185 nucleotides (395 amino acids; deduced M(r) 44,669 Da). The Belém VP6 gene demonstrated 97.9% nucleotide homology with the human group C/Bristol VP6 gene and 83.4% nucleotide homology (91.6% deduced amino acid homology) with the corrected porcine group C/Cowden sequence. The Preston VP6 gene demonstrated 99.6% nucleotide homology with the human group C/Bristol VP6 gene and 84.0% nucleotide homology (91.6% deduced amino acid homology) with the corrected porcine group C/Cowden sequence. Remarkably, the deduced amino acid sequence of the Brazilian strain was identical to that of the U.K. isolates.
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Affiliation(s)
- S J Cooke
- Department of Microbiology, University Medical School, Southampton General Hospital, U.K
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50
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Abstract
A novel, sequence-independent strategy has been developed for the amplification of full-length cDNA copies of the genes of double-stranded RNA (dsRNA) viruses. Using human (Bristol) group C rotavirus as an example, a single amino-linked modified oligonucleotide (primer 1) was ligated to either end of each dsRNA genome segment by using T4 RNA ligase. Following reverse transcription, annealing, and repair of cDNA strands, amplification of the viral dsRNA genome was accomplished by polymerase chain reaction using a single complementary oligonucleotide (primer 2). Northern (RNA) hybridization of cDNA to virus dsRNA indicated that it was possible to generate cDNA representing the complete genome from very small clinical samples. This technique was used to determine the complete nucleotide sequence (728 bp) and coding assignment of gene 10, which revealed an open reading frame of 212 amino acids with limited homology to NS26 from human group A rotavirus. In contrast to previous tailing methods, the addition of one defined primer allowed unequivocal identification of terminal nucleotides and should be generally applicable to viruses with segmented dsRNA genomes and especially for analysis of clinical samples, for which very limited quantities of biological material are available.
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Affiliation(s)
- P R Lambden
- Department of Microbiology, University of Southampton Medical School, Southampton General Hospital, United Kingdom
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