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4. COVID-19: Rapid antigen detection for SARS-CoV-2 by lateral flow assay: A national systematic evaluation of sensitivity and specificity for mass-testing

Author

Peto, T., Affron, D., Afrough, B., Agasu, A., Ainsworth, M., Allanson, A., Allen, K., Allen, C., Archer, L., Ashbridge, N., Aurfan, I., Avery, M., Badenoch, E., Bagga, P., Balaji, R., Baldwin, E., Barraclough, S., Beane, C., Bell, J., Benford, T., Bird, S., Bishop, M., Bloss, A., Body, R., Boulton, R., Bown, A., Bratten, C., Bridgeman, C., Britton, D., Brooks, T., Broughton-Smith, M., Brown, P., Buck, B., Butcher, E., Byrne, W., Calderon, G., Campbell, S., Carr, O., Carter, P., Carter, D., Cathrall, M., Catton, M., Chadwick, J., Chapman, D., Chau, K.K., Chaudary, T., Chidavaenzi, S., Chilcott, S., Choi, B., Claasen, H., Clark, S., Clarke, R., Clarke, D., Clayton, R., Collins, K., Colston, R., Connolly, J., Cook, E., Corcoran, M., Corley, B., Costello, L., Coulson, C., Crook, A., Crook, D.W., D'Arcangelo, S., Darby, M-A, Davis, J., de Koning, R., Derbyshire, P., Devall, P., Dolman, M., Draper, N., Driver, M., Dyas, S., Eaton, E., Edwards, J., Elderfield, R., Ellis, K., Ellis, G., Elwell, S., Evans, R., Evans, B., Evans, M., Eyre, D., Fahey, C., Fenech, V., Field, J., Field, A., Foord, T., Fowler, T., French, M., Fuchs, H., Gan, J., Gernon, J., Ghadiali, G., Ghuman, N., Gibbons, K., Gill, G., Gilmour, K., Goel, A., Gordon, S., Graham, T., Grassam-Rowe, A., Green, D., Gronert, A., Gumsley-Read, T., Hall, C., Hallis, B., Hammond, S., Hammond, P., Hanney, B., Hardy, V., Harker, G., Harris, A., Havinden-Williams, M., Hazell, E., Henry, J., Hicklin, K., Hollier, K., Holloway, B., Hoosdally, S.J., Hopkins, S., Hughes, L., Hurdowar, S., Hurford, S-A, Jackman, J., Jackson, H., Johns, R., Johnston, S., Jones, J., Kanyowa, T., Keating-Fedders, K., Kempson, S., Khan, I., Khulusi, B., Knight, T., Krishna, A., Lahert, P., Lampshire, Z., Lasserson, D., Lee, K., Lee, L.Y.W., Legard, A., Leggio, C., Liu, J., Lockett, T., Logue, C., Lucas, V., Lumley, S.F., Maripuri, V., Markham, D., Marshall, E., Matthews, P.C., Mckee, S., McKee, D.F., McLeod, N., McNulty, A., Mellor, F., Michel, R., Mighiu, A., Miller, J., Mirza, Z., Mistry, H., Mitchell, J., Moeser, M.E., Moore, S., Muthuswamy, A., Myers, D., Nanson, G., Newbury, M., Nicol, S., Nuttall, H., Nwanaforo, J.J., Oliver, L., Osbourne, W., Osbourne, J., Otter, A., Owen, J., Panchalingam, S., Papoulidis, D., Pavon, J.D., Peace, A., Pearson, K., Peck, L., Pegg, A., Pegler, S., Permain, H., Perumal, P., Peto, L., Peto, T.E.A., Pham, T., Pickford, H.L., Pinkerton, M., Platton, M., Price, A., Protheroe, E., Purnell, H., Rawden, L., Read, S., Reynard, C., Ridge, S., Ritter, T.G., Robinson, J., Robinson, P., Rodger, G., Rowe, C., Rowell, B., Rowlands, A., Sampson, S., Saunders, K., Sayers, R., Sears, J., Sedgewick, R., Seeney, L., Selassie, A., Shail, L., Shallcross, J., Sheppard, L., Sherkat, A., Siddiqui, S., Sienkiewicz, A., Sinha, L., Smith, J., Smith, E., Stanton, E., Starkey, T., Stawiarski, A., Sterry, A., Stevens, J., Stockbridge, M., Stoesser, N., Sukumaran, A., Sweed, A., Tatar, S., Thomas, H., Tibbins, C., Tiley, S., Timmins, J., Tomas-Smith, C., Topping, O., Turek, E., Neibler, T., Trigg-Hogarth, K., Truelove, E., Turnbull, C., Tyrrell, D., Vaughan, A., Vertannes, J., Vipond, R., Wagstaff, L., Waldron, J., Walker, P., Walker, A.S., Walters, M., Wang, J.Y., Watson, E., Webberley, K., Webster, K., Westland, G., Wickens, I., Willcocks, J., Willis, H., Wilson, S., Wilson, B., Woodhead, L., Wright, D., Xavier, B., Yelnoorkar, F., Zeidan, L., Zinyama, R., Peto, T., Affron, D., Afrough, B., Agasu, A., Ainsworth, M., Allanson, A., Allen, K., Allen, C., Archer, L., Ashbridge, N., Aurfan, I., Avery, M., Badenoch, E., Bagga, P., Balaji, R., Baldwin, E., Barraclough, S., Beane, C., Bell, J., Benford, T., Bird, S., Bishop, M., Bloss, A., Body, R., Boulton, R., Bown, A., Bratten, C., Bridgeman, C., Britton, D., Brooks, T., Broughton-Smith, M., Brown, P., Buck, B., Butcher, E., Byrne, W., Calderon, G., Campbell, S., Carr, O., Carter, P., Carter, D., Cathrall, M., Catton, M., Chadwick, J., Chapman, D., Chau, K.K., Chaudary, T., Chidavaenzi, S., Chilcott, S., Choi, B., Claasen, H., Clark, S., Clarke, R., Clarke, D., Clayton, R., Collins, K., Colston, R., Connolly, J., Cook, E., Corcoran, M., Corley, B., Costello, L., Coulson, C., Crook, A., Crook, D.W., D'Arcangelo, S., Darby, M-A, Davis, J., de Koning, R., Derbyshire, P., Devall, P., Dolman, M., Draper, N., Driver, M., Dyas, S., Eaton, E., Edwards, J., Elderfield, R., Ellis, K., Ellis, G., Elwell, S., Evans, R., Evans, B., Evans, M., Eyre, D., Fahey, C., Fenech, V., Field, J., Field, A., Foord, T., Fowler, T., French, M., Fuchs, H., Gan, J., Gernon, J., Ghadiali, G., Ghuman, N., Gibbons, K., Gill, G., Gilmour, K., Goel, A., Gordon, S., Graham, T., Grassam-Rowe, A., Green, D., Gronert, A., Gumsley-Read, T., Hall, C., Hallis, B., Hammond, S., Hammond, P., Hanney, B., Hardy, V., Harker, G., Harris, A., Havinden-Williams, M., Hazell, E., Henry, J., Hicklin, K., Hollier, K., Holloway, B., Hoosdally, S.J., Hopkins, S., Hughes, L., Hurdowar, S., Hurford, S-A, Jackman, J., Jackson, H., Johns, R., Johnston, S., Jones, J., Kanyowa, T., Keating-Fedders, K., Kempson, S., Khan, I., Khulusi, B., Knight, T., Krishna, A., Lahert, P., Lampshire, Z., Lasserson, D., Lee, K., Lee, L.Y.W., Legard, A., Leggio, C., Liu, J., Lockett, T., Logue, C., Lucas, V., Lumley, S.F., Maripuri, V., Markham, D., Marshall, E., Matthews, P.C., Mckee, S., McKee, D.F., McLeod, N., McNulty, A., Mellor, F., Michel, R., Mighiu, A., Miller, J., Mirza, Z., Mistry, H., Mitchell, J., Moeser, M.E., Moore, S., Muthuswamy, A., Myers, D., Nanson, G., Newbury, M., Nicol, S., Nuttall, H., Nwanaforo, J.J., Oliver, L., Osbourne, W., Osbourne, J., Otter, A., Owen, J., Panchalingam, S., Papoulidis, D., Pavon, J.D., Peace, A., Pearson, K., Peck, L., Pegg, A., Pegler, S., Permain, H., Perumal, P., Peto, L., Peto, T.E.A., Pham, T., Pickford, H.L., Pinkerton, M., Platton, M., Price, A., Protheroe, E., Purnell, H., Rawden, L., Read, S., Reynard, C., Ridge, S., Ritter, T.G., Robinson, J., Robinson, P., Rodger, G., Rowe, C., Rowell, B., Rowlands, A., Sampson, S., Saunders, K., Sayers, R., Sears, J., Sedgewick, R., Seeney, L., Selassie, A., Shail, L., Shallcross, J., Sheppard, L., Sherkat, A., Siddiqui, S., Sienkiewicz, A., Sinha, L., Smith, J., Smith, E., Stanton, E., Starkey, T., Stawiarski, A., Sterry, A., Stevens, J., Stockbridge, M., Stoesser, N., Sukumaran, A., Sweed, A., Tatar, S., Thomas, H., Tibbins, C., Tiley, S., Timmins, J., Tomas-Smith, C., Topping, O., Turek, E., Neibler, T., Trigg-Hogarth, K., Truelove, E., Turnbull, C., Tyrrell, D., Vaughan, A., Vertannes, J., Vipond, R., Wagstaff, L., Waldron, J., Walker, P., Walker, A.S., Walters, M., Wang, J.Y., Watson, E., Webberley, K., Webster, K., Westland, G., Wickens, I., Willcocks, J., Willis, H., Wilson, S., Wilson, B., Woodhead, L., Wright, D., Xavier, B., Yelnoorkar, F., Zeidan, L., and Zinyama, R.

Abstract

Background Lateral flow device (LFD) viral antigen immunoassays have been developed around the world as diagnostic tests for SARS-CoV-2 infection. They have been proposed to deliver an infrastructure-light, cost-economical solution giving results within half an hour. Methods LFDs were initially reviewed by a Department of Health and Social Care team, part of the UK government, from which 64 were selected for further evaluation from 1st August to 15th December 2020. Standardised laboratory evaluations, and for those that met the published criteria, field testing in the Falcon-C19 research study and UK pilots were performed (UK COVID-19 testing centres, hospital, schools, armed forces). Findings 4/64 LFDs so far have desirable performance characteristics (orient Gene, Deepblue, Abbott and Innova SARS-CoV-2 Antigen Rapid Qualitative Test). All these LFDs have a viral antigen detection of >90% at 100,000 RNA copies/ml. 8951 Innova LFD tests were performed with a kit failure rate of 5.6% (502/8951, 95% CI: 5.1–6.1), false positive rate of 0.32% (22/6954, 95% CI: 0.20–0.48). Viral antigen detection/sensitivity across the sampling cohort when performed by laboratory scientists was 78.8% (156/198, 95% CI 72.4–84.3). Interpretation Our results suggest LFDs have promising performance characteristics for mass population testing and can be used to identify infectious positive individuals. The Innova LFD shows good viral antigen detection/sensitivity with excellent specificity, although kit failure rates and the impact of training are potential issues. These results support the expanded evaluation of LFDs, and assessment of greater access to testing on COVID-19 transmission. Funding Department of Health and Social Care. University of Oxford. Public Health England Porton Down, Manchester University NHS Foundation Trust, National Institute of Health Research.

Published
2021

33. Structural basis of dynamic glycine receptor clustering

Author

Sola, M., primary, Bavro, V.N., additional, Timmins, J., additional, Franz, T., additional, Ricard-Blum, S., additional, Schoehn, G., additional, Ruigrok, R.W.H., additional, Paarmann, I., additional, Saiyed, T., additional, and O'Sullivan, G.A., additional

Published
2004
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35. Education and labour productivity in New Zealand.

Author

Razzak, W.A. and Timmins, J.

Abstract

We estimate the effect of four types of education qualifications, as a proxy for human capital and skill levels, on GDP per capita, and compute the average percentage returns. We also test the effect of the product of each proxy of human capital with R&D on GDP per capita. We find that only university qualification and its product with R&D to have a positive effect on the average economy-wide productivity. [ABSTRACT FROM AUTHOR]

Published
2010
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38. CONCENTRATION AND INTEGRATION IN THE SHEFFIELD CRUCIBLE STEEL INDUSTRY.

Author

Timmins, J. G.

Subjects
INDUSTRIAL concentration, STEEL industry, BUSINESS enterprises, BUSINESS expansion, BUSINESS, HILLSBOROUGH Stadium Disaster, Sheffield, England, 1989
Abstract

The article focuses on the scale of operations and the extent of integration in the steel industry in Sheffield, England. It is commonly held that before the adoption of bulk steel making during the second half of the nineteenth century, the Sheffield steel industry was characterized by small-scale enterprise. For more than a century the expansion of the Sheffield steel industry was achieved largely by means of the endeavors of many relatively small concerns operating with comparatively little capital and often in very restricted premises. More recently, Dr A. Birch has restated this viewpoint, remarking, additionally, on the structure of steel making firms. The history of the steel industry in Sheffield in the first half of the nineteenth century is of the building up of small-scale concerns in the backyards and orchards of the houses in the town. There was a great proliferation of small concerns specializing in the business of converting and refining. Although Dr. Birch over-simplifies, the emphasis, he and Professor G.P. Jones have placed on the numerical predominance of small-scale production units in the industry cannot be disputed.

Published
1982
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39. Failure of epoprostenol (prostacyclin, PGI2) to inhibit platelet aggregation and to prevent restenosis after coronary angioplasty: results of a randomised placebo controlled trial.

Author

Gershlick, A. H., Spriggins, D., Davies, S. W., Syndercombe Court, Y. D., Timmins, J., Timmis, A. D., Rothman, M. T., Layton, C., and Balcon, R.

Abstract

OBJECTIVE--To study the effect of epoprostenol (prostacyclin, PGI2) given before, during, and for 36 h after coronary angioplasty on restenosis at six months and to evaluate the transcardiac gradient of platelet aggregation before and after percutaneous transluminal coronary angioplasty (PTCA) in treated and placebo groups. DESIGN--Double blind placebo controlled randomised study. PATIENTS--135 patients with successful coronary angioplasty. METHODS--Intravenous infusion of PGI2 (4 ng/kg/ml) or buffer was started before balloon angioplasty and continued for 36 hours. Platelet aggregation was measured in blood from the aorta and coronary sinus before and after PTCA in each group. Routine follow up was at six months with repeat angiography and there was quantitative assessment of all angiograms (those undertaken within the follow up period and at routine follow up). PRESENTATION OF RESULTS--Restenosis rates in treated and placebo groups determined according to the National Heart, Lung and Blood Institute definition IV. Comparison at follow up between the effect of treatment on mean absolute luminal diameter and mean absolute follow up diameter in the placebo group. Comparison of acute gain and late loss between groups. RESULTS--Of 125 patients available for assessment 23 were re-admitted because of angina within the follow up period. Quantitative angiography showed restenosis in 15 (10 in the PGI2 group and five in the placebo group). Of 105 patients evaluated at six month angiography there was restenosis in nine more in the PGI2 group and 18 more in the placebo group. Total restenosis rates (for patients) were 29.2% for PGI2 and 38.3% for placebo (NS). The mean absolute gain in luminal diameter was 1.84 (0.76) mm in the PGI2 group and 1.58 (0.56) mm in the placebo group (p = 0.04); the late loss in the PGI2 group was also greater (0.65 (0.94) mm vs 0.62 (0.89) mm (NS) and there was no significant difference in final luminal diameter at follow up between the two groups (1.83 (0.88) mm v 1.59 (0.60) mm). The transcardiac gradient of quantitative platelet aggregation increased after PTCA in both groups, indicating that PGI2 in this dose did not affect angioplasty-induced platelet activation. Mean (SD) platelet activation indices in the PGI2 group were pre PTCA aorta 8.4 (4.1) v coronary sinus 8.8 (4.0) (p = 0.001) and post PTCA aorta 8.9(3.0) v coronary sinus 12.9 (5.7) (p = 0.001). In the placebo group the values were pre PTCA aorta 7.6 (3.3) v coronary sinus 7.4 (3.6) (p = 0.001) and post PTCA aorta 7.6(2.8) v coronary sinus 11.2(4.3) (p = 0.001). CONCLUSION--The dose of PGI2 given was designed to limit side effects and as a short-term infusion did not significantly decrease the six month restenosis rate after PTCA. The sample size, which was determined by the original protocol and chosen because of the potency of the agent being tested, would have detected only a 50% reduction in restenosis rate. There was, however, no effect in the treated patients on the increased platelet aggregation seen in placebo group as a result of angioplasty. Angioplasty is a powerful stimulus to blood factor activation. Powerful agents that prevent local platelet adhesion and aggregation are likely to be required to reduce restenosis. [ABSTRACT FROM PUBLISHER]

Published
1994
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40. Evaluation of pseudorabies virus glycoprotein gp50 as a vaccine for Aujeszky's disease in mice and swine: expression by vaccinia virus and Chinese hamster ovary cells

Author

Marchioli, C C, Yancey, R J, Petrovskis, E A, Timmins, J G, and Post, L E

Abstract

Pseudorabies virus (PRV) is an alphaherpesvirus which causes an economically important disease of swine. One of the PRV glycoproteins, gp50, was previously identified as the sequence homolog of herpes simplex virus glycoprotein gD (E.A. Petrovskis, J.G. Timmins, M.A. Armentrout, C.C. Marchioli, R.J. Yancey, Jr., and L.E. Post, J. Virol. 59:216-223, 1986). gp50 was evaluated as a PRV subunit vaccine candidate. gp50 protected mice from PRV-induced mortality either when delivered via infection with a recombinant vaccinia virus or when administered as a subunit vaccine produced in a eucaryotic cell line, Chinese hamster ovary (CHO) cells. In addition, gp50 synthesized in CHO cells protected pigs from lethal infection with PRV. This result demonstrates that a single viral glycoprotein could induce a protective immune response in the natural host of a herpesvirus infection.

Published
1987
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41. Deletions in vaccine strains of pseudorabies virus and their effect on synthesis of glycoprotein gp63

Author

Petrovskis, E A, Timmins, J G, Gierman, T M, and Post, L E

Abstract

The pseudorabies virus vaccine strains Norden and Bartha each have been reported to have deletions in the small unique component of the genome (B. Lomniczi, M. L. Blankenship, and T. Ben-Porat, J. Virol. 49:970-979, 1984). The deletion in Norden was shown to delete the entire coding region for gI but not any of the coding sequences for gp63. However, gp63 in Norden-infected cells was only 36 kilodaltons, and a 44-kilodalton form of gp63 was released into the medium. In Bartha, the deletion removed the coding region for all but 89 amino acids of gp63, and no gp63 was detected in either Bartha-infected cells or medium.

Published
1986
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42. Use of lambda gt11 to isolate genes for two pseudorabies virus glycoproteins with homology to herpes simplex virus and varicella-zoster virus glycoproteins

Author

Petrovskis, E A, Timmins, J G, and Post, L E

Abstract

A library of pseudorabies virus (PRV) DNA fragments was constructed in the expression cloning vector lambda gt11. The library was screened with antisera which reacted with mixtures of PRV proteins to isolate recombinant bacteriophages expressing PRV proteins. By the nature of the lambda gt11 vector, the cloned proteins were expressed in Escherichia coli as beta-galactosidase fusion proteins. The fusion proteins from 35 of these phages were purified and injected into mice to raise antisera. The antisera were screened by several different assays, including immunoprecipitation of [14C]glucosamine-labeled PRV proteins. This method identified phages expressing three different PRV glycoproteins: the secreted glycoprotein, gX; gI; and a glycoprotein that had not been previously identified, which we designate gp63. The gp63 and gI genes map adjacent to each other in the small unique region of the PRV genome. The DNA sequence was determined for the region of the genome encoding gp63 and gI. It was found that gp63 has a region of homology with a herpes simplex virus type 1 (HSV-1) protein, encoded by US7, and also with varicella-zoster virus (VZV) gpIV. The gI protein sequence has a region of homology with HSV-1 gE and VZV gpI. It is concluded that PRV, HSV, and VZV all have a cluster of homologous glycoprotein genes in the small unique components of their genomes and that the organization of these genes is conserved.

Published
1986
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43. DNA sequence of the gene for pseudorabies virus gp50, a glycoprotein without N-linked glycosylation

Author

Petrovskis, E A, Timmins, J G, Armentrout, M A, Marchioli, C C, Yancey, R J, and Post, L E

Abstract

The DNA sequence was determined for a region of the pseudorabies virus (PRV) genome to which a mutation defining resistance to a monoclonal antibody has been mapped (M. W. Wathen and L. M. K. Wathen, J. Virol., 51:57-62, 1984). This sequence was found to contain an open reading frame that did not include an amino acid sequence directing N-linked glycosylation. This open reading frame was expressed in uninfected Chinese hamster ovary cells to produce the PRV glycoprotein gp50. When PRV-infected Vero cells were incubated in the presence of tunicamycin, the gp50 that was produced had an identical molecular weight to that produced in the absence of drug. When infected cells were incubated in the presence of monensin, the molecular weight of gp50 was reduced from 60,000 to 45,000, but was not sensitive to endo-beta-N-acetylglucosaminidase H. These observations led to the conclusion that gp50 does not contain N-linked carbohydrate, as predicted from the DNA sequence. A region of the amino acid sequence and the positions of the cysteine residues of PRV gp50 are homologous to glycoprotein D of herpes simplex virus.

Published
1986
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44. Mapping and sequence of the gene for the pseudorabies virus glycoprotein which accumulates in the medium of infected cells

Author

Rea, T J, Timmins, J G, Long, G W, and Post, L E

Abstract

RNA from pseudorabies virus (PRV)-infected cells was translated in a reticulocyte lysate with and without the addition of dog pancreas microsomes. Upon addition of the microsomes to the translation reaction, an additional prominent protein product was observed that was not present when microsomes were omitted. The gene coding for this processed protein and its lower-molecular-weight precursor was mapped within the small unique region of the genome by hybridization of mRNA to cloned fragments of PRV DNA and translation of the selected mRNAs. A fragment of the coding region of this gene was inserted into an open reading frame cloning vector to express part of this gene as a hybrid protein in Escherichia coli. This hybrid protein was injected into mice to raise an antiserum which was found to precipitate the glycoprotein which accumulates in the medium of PRV-infected cells. This allows us to conclude that the gene for the "excreted" glycoprotein (gX) maps to the small unique region of the genome, and that the precursor of this glycoprotein is readily processed by dog pancreas microsomes. The region of the PRV genome which codes for this glycoprotein was sequenced and found to include an open reading frame coding for 498 amino acids, flanked by sequences which contain features common to eucaryotic promoters and polyadenylation signals. The predicted protein sequence includes a hydrophobic sequence at the N-terminus which could be a signal sequence, and a hydrophobic sequence followed by a hydrophilic sequence at the C-terminus.

Published
1985
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50. Stress-induced nucleoid remodeling in Deinococcus radiodurans is associated with major changes in Heat Unstable (HU) protein dynamics.

Author

Vauclare P, Wulffelé J, Lacroix F, Servant P, Confalonieri F, Kleman JP, Bourgeois D, and Timmins J

Subjects
DNA, Bacterial metabolism, DNA, Bacterial genetics, Stress, Physiological, Ultraviolet Rays, Bacterial Proteins metabolism, Bacterial Proteins genetics, Deinococcus radiation effects, Deinococcus genetics, Deinococcus metabolism, DNA-Binding Proteins metabolism, DNA-Binding Proteins genetics
Abstract

Bacteria have developed a wide range of strategies to respond to stress, one of which is the rapid large-scale reorganization of their nucleoid. Nucleoid associated proteins (NAPs) are believed to be major actors in nucleoid remodeling, but the details of this process remain poorly understood. Here, using the radiation resistant bacterium D. radiodurans as a model, and advanced fluorescence microscopy, we examined the changes in nucleoid morphology and volume induced by either entry into stationary phase or exposure to UV-C light, and characterized the associated changes in mobility of the major NAP in D. radiodurans, the heat-unstable (HU) protein. While both types of stress induced nucleoid compaction, HU diffusion was reduced in stationary phase cells, but was instead increased following exposure to UV-C, suggesting distinct underlying mechanisms. Furthermore, we show that UV-C-induced nucleoid remodeling involves a rapid nucleoid condensation step associated with increased HU diffusion, followed by a slower decompaction phase to restore normal nucleoid morphology and HU dynamics, before cell division can resume. These findings shed light on the diversity of nucleoid remodeling processes in bacteria and underline the key role of HU in regulating this process through changes in its mode of assembly on DNA., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2024
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