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3. Irish SARS-CoV-2 convalescent serological status of children following acute pneumonia during Ireland’s first wave

Author

Irfan, S. Sabir, Flinn, K., Mullane, David, Murray, Deirdre M., Linnane, B., Holder, P., De Gascun, C., and Ní ­Chróinín, Muireann

Subjects
SARS-CoV-2, COVID-19, Epidemic, Ireland, Children
Abstract

A global epidemic caused by a novel coronavirus (SARS-CoV-2) in China in December 2019 has spread worldwide¹. We hypothesised that due to low levels of viral shedding in children's upper airways, many children with COVID-19 related respiratory illness admitted to the hospital might be negative on nasopharyngeal PCR testing. Evidence suggests that SARS-CoV-2 antibodies can be detected typically 9-14 days after onset of symptoms but may take up to 3 months2. Therefore, convalescent serological evidence of SARS-CoV-2, as an alternative means to determine the rate of COVID-19 infection, was assessed.

Published
2022

4. Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021

Author

Funk T., Pharris A., Spiteri G., Bundle N., Melidou A., Carr M., Gonzalez G., Garcia-Leon A., Crispie F., O'Connor L., Murphy N., Mossong J., Vergison A., Wienecke-Baldacchino A. K., Abdelrahman T., Riccardo F., Stefanelli P., Di Martino A., Bella A., Lo Presti A., Casaca P., Moreno J., Borges V., Isidro J., Ferreira R., Gomes J. P., Dotsenko L., Suija H., Epstein J., Sadikova O., Sepp H., Ikonen N., Savolainen-Kopra C., Blomqvist S., Mottonen T., Helve O., Gomes-Dias J., Adlhoch C., Macori G., Russell L., Yandle Z., Bennett C., O'Byrne E., Murphy A., Tuite G., Conroy A., Duffy M., Morley U., Keoghan B., Ford I., Kennedy M., McDonnell S., Flynn A., Clarke A., Crowley A., Martin C., Kelly E., Foxton J., Hare D., Dunford L., Connell J., Moran J., Dean J., Fanning S., Rajan L., De Gascun C., Kenny J., Cotter P., Walsh C., Lawton E., Fitzpatrick A., Mullins E., Della Bartola M., McCabe M., Stapleton P., Meaney C., Fanning L., Prentice M., MacSharry J., Dempsey C., Mallon P., Leon A., Chaturvedi A., Coughlan S., McAndrew G., Reddington K., Walsh F., Fitzpatrick D., Smyth C., O'Dwyer T., Chambers T., Clarke L., Jebb D., Klopp J., Kavanagh D., Haslam K., Buckley P., Lemass K., Fitzpatrick F., Burns K., Cafferkey J., Richmond A., Foley M., Sanchez-Morgado J., Chalapati S., Pinnamaneni N., Crosbie C., Limbachiya D., Tinago W., Garcia Leon A. A., Miles S., Alalwan D., Negi R., Macken A., Feeney E., Kenny G., McCann K., Kelly N., Blair M., McCann R., Kenny C., O'Brion C., Waqas S., Savinelli S., Doran P., Bracken T., Varghese P., Lambert J. S., Cotter A., Muldoon E., Sheehan G., McGinty T., Lambert J., Green S., Leamy K., de Barra E., McConkey S., Kelly C., Horgan M., Sadlier C., Yousif O., O'Donnell J., Fitzgerald M., Petty-Saphon N., Cuddihy J., Fiore S., Fabiani C., Benedetti E., Di Mario G., Facchini M., Puzelli S., Calzoletti L., Fontana S., Venturi G., Fortuna C., Marsili G., Amendola A., Stuppia L., Savini G., Picerno A., Lopizzo T., Dell'Edera D., Minchella P., Greco F., Mauro M. V., Viglietto G., Atripaldi L., Limone A., D'Agaro P., Licastro D., Marcello A., Capobianchi M. R., Icardi G., Bruzzone B., Lillo F., Orsi A., Pariani E., Baldanti F., Gismondo M. R., Maggi F., Caruso A., Ceriotti F., Boniotti B., Bagnarelli P., Garofalo S., Scutella M., Pagani E., Collini L., Ghisetti V., Ru G., Chironna M., Parisi A., Rubino S., Serra C., Piras G., Coghe F., Vitale F., Tramuto F., Scalia G., Palermo C. I., Mancuso G., Di Gaudio F., Vullo S., Reale S., Cusi M. G., Rossolini G. M., Pistello M., Mencacci A., Camilloni B., Severini S., Di Benedetto M., Calogero T., Monne I., Biscaro V., COVID Study Groups, Funk T., Pharris A., Spiteri G., Bundle N., Melidou A., Carr M., Gonzalez G., Garcia-Leon A., Crispie F., O'Connor L., Murphy N., Mossong J., Vergison A., Wienecke-Baldacchino A.K., Abdelrahman T., Riccardo F., Stefanelli P., Di Martino A., Bella A., Lo Presti A., Casaca P., Moreno J., Borges V., Isidro J., Ferreira R., Gomes J.P., Dotsenko L., Suija H., Epstein J., Sadikova O., Sepp H., Ikonen N., Savolainen-Kopra C., Blomqvist S., Mottonen T., Helve O., Gomes-Dias J., Adlhoch C., Macori G., Russell L., Yandle Z., Bennett C., O'Byrne E., Murphy A., Tuite G., Conroy A., Duffy M., Morley U., Keoghan B., Ford I., Kennedy M., McDonnell S., Flynn A., Clarke A., Crowley A., Martin C., Kelly E., Foxton J., Hare D., Dunford L., Connell J., Moran J., Dean J., Fanning S., Rajan L., De Gascun C., Kenny J., Cotter P., Walsh C., Lawton E., Fitzpatrick A., Mullins E., Della Bartola M., McCabe M., Stapleton P., Meaney C., Fanning L., Prentice M., MacSharry J., Dempsey C., Mallon P., Leon A., Chaturvedi A., Coughlan S., McAndrew G., Reddington K., Walsh F., Fitzpatrick D., Smyth C., O'Dwyer T., Chambers T., Clarke L., Jebb D., Klopp J., Kavanagh D., Haslam K., Buckley P., Lemass K., Fitzpatrick F., Burns K., Cafferkey J., Richmond A., Foley M., Sanchez-Morgado J., Chalapati S., Pinnamaneni N., Crosbie C., Limbachiya D., Tinago W., Garcia Leon A.A., Miles S., Alalwan D., Negi R., Macken A., Feeney E., Kenny G., McCann K., Kelly N., Blair M., McCann R., Kenny C., O'Brion C., Waqas S., Savinelli S., Doran P., Bracken T., Varghese P., Lambert J.S., Cotter A., Muldoon E., Sheehan G., McGinty T., Lambert J., Green S., Leamy K., de Barra E., McConkey S., Kelly C., Horgan M., Sadlier C., Yousif O., O'Donnell J., Fitzgerald M., Petty-Saphon N., Cuddihy J., Fiore S., Fabiani C., Benedetti E., Di Mario G., Facchini M., Puzelli S., Calzoletti L., Fontana S., Venturi G., Fortuna C., Marsili G., Amendola A., Stuppia L., Savini G., Picerno A., Lopizzo T., Dell'Edera D., Minchella P., Greco F., Mauro M.V., Viglietto G., Atripaldi L., Limone A., D'Agaro P., Licastro D., Marcello A., Capobianchi M.R., Icardi G., Bruzzone B., Lillo F., Orsi A., Pariani E., Baldanti F., Gismondo M.R., Maggi F., Caruso A., Ceriotti F., Boniotti B., Bagnarelli P., Garofalo S., Scutella M., Pagani E., Collini L., Ghisetti V., Ru G., Chironna M., Parisi A., Rubino S., Serra C., Piras G., Coghe F., Vitale F., Tramuto F., Scalia G., Palermo C.I., Mancuso G., Di Gaudio F., Vullo S., Reale S., Cusi M.G., Rossolini G.M., Pistello M., Mencacci A., Camilloni B., Severini S., Di Benedetto M., Calogero T., Monne I., Biscaro V., and COVID Study Groups

Subjects
Infecções Respiratórias, 2019-20 coronavirus outbreak, medicine.medical_specialty, Coronavirus disease 2019 (COVID-19), Critical Care, Epidemiology, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), variants of concern, Settore MED/42 - Igiene Generale E Applicata, 03 medical and health sciences, 0302 clinical medicine, Virology, Internal medicine, Medicine, Humans, Intensive care admission, 030212 general & internal medicine, COVID-19, Europe, SARS-CoV-2, surveillance, Surveillance, business.industry, 030503 health policy & services, Public Health, Environmental and Occupational Health, Odds ratio, Confidence interval, Variants of Concern, COVID-19, Europe, SARS-CoV-2, surveillance, variants of concern, 0305 other medical science, business, Rapid Communication, Human
Abstract

COVID study groups - PORTUGAL: Portuguese Laboratory Network for the Diagnosis of COVID-19 and Public Health Department of the Health Administrative Regions, Physicians that provided data and samples from suspected cases and SARS-CoV-2 genetic characterization. INSA laboratory team for the diagnosis of SARS-CoV-2. Algarve Biomedical Center and Unilabs. We compared 19,207 cases of SARS-CoV-2 variant B.1.1.7/S gene target failure (SGTF), 436 B.1.351 and 352 P.1 to non-variant cases reported by seven European countries. COVID-19 cases with these variants had significantly higher adjusted odds ratios for hospitalisation (B.1.1.7/SGTF: 1.7, 95% confidence interval (CI): 1.0-2.9; B.1.351: 3.6, 95% CI: 2.1-6.2; P.1: 2.6, 95% CI: 1.4-4.8) and B.1.1.7/SGTF and P.1 cases also for intensive care admission (B.1.1.7/SGTF: 2.3, 95% CI: 1.4-3.5; P.1: 2.2, 95% CI: 1.7-2.8). ECDC internal funds. The ICSC and the AIID Cohort are supported by Science Foundation Ireland under the Science Foundation Ireland, Enterprise Ireland, IDA Ireland COVID-19 Rapid Response Funding Call (Grant number: COVID-RRC 20/COV/0103 and COVID-RRC 20/COV/0305). info:eu-repo/semantics/publishedVersion

Published
2021

7. National scientific medical meeting 1997 abstracts

Author

Willison, H. J., Lastovica, A. J., Prendergast, M. M., Moran, A. P., Walsh, C., Flitcroft, I., Eustace, P., McMahon, C., Smith, J., Smith, O. P., Lakshmandass, G., Taylor, M. R. H., Holland, C. V., Cox, D., Good, B., Kearns, G. M., Gaffney, P., Shark, K., Frauenshuh, M., Ortmann, W., Messner, R., King, R., Rich, S., Behrens, T., Mahmud, N., Molloy, A., McPartlin, J., Scott, J. M., Weir, D. G., Walsh, K. M., Thorburn, D., Mills, P., Morris, A. J., Good, T., Cameron, S., McCruden, E. A. B., Bennett, M. W., O’Connell, J., Brady, C., Roche, D., Collins, J. K., Shanahan, F., O’Sullivant, G. C., Henry, M., Koston, S., McMahon, K., MacNee, W., FitzGerald, M. X., O’Connor, C. M., McGonagle, D., Gibbon, W., O’Connor, P., Emery, P., Murphy, M., Watson, R., Casey, E., Naidu, E., Murphy, M., Watson, R., Barnes, L., McCann, S., Murphy, M., Watson, R., Barnes, L., Sweeney, E., Barrett, E. J., Graham, H., Cunningham, R. T., Johnston, C. F., Curry, W. J., Buchanan, K. D., Courtney, C. H., McAllister, A. S., McCance, D. R., Hadden, D. R., Bell, P. M., Leslie, H., Sheridan, B., Atkinson, A. B., Kilbane, M. T., Smith, D. F., Murray, M. J., Shering, S. G., McDermott, E. W. M., O’Higgins, N. J., Smyth, P. P. A., McEneny, J., Trimble, E. R., Young, I. S., Sharpe, P., Mercer, C., McMaster, D., Young, I. S., Evans, A. E., Young, I. S., Cundick, J., Hasselwander, O., McMaster, D., McGeough, J., Savage, D., Maxwell, A. P., Evans, A. E., Kee, F., Larkin, C. J., Watson, R. G. P., Johnston, C., Ardill, J. E. S., Buchanan, K. D., McNamara, D. A., Walsh, T. N., Bouchier-Hayes, D. J., Madden, C., Timon, C., Gardiner, N., Lawler, M., O’Riordan, J., Duggan, C., McCann, S. R., Gowing, H., Braakman, E., Lawler, M., Byrne, C., Martens, A. C. M., Hagenbeek, A., McCann, S. R., Kinsella, N., Cusack, S., Lawler, M., Baker, H., White, B., Smith, O. P., Lawler, M., Gardiner, N., Molloy, K., Gowing, H., Wogan, A., McCann, S. R., McElwaine, S., Lawler, M., Hollywood, D., McCann, S. R., Mcmahon, C., Merry, C., Ryan, M., Smith, O., Mulcahy, F. M., Murphy, C., Briones, J., Gardiner, N., McCann, S. R., Lawler, M., White, B., Lawler, M., Cusack, S., Kinsella, N., Smith, O. P., Lavin, P., McCaffrey, M., Gillen, P., White, B., Smith, O. P., Thompson, L., Lalloz, M., Layton, M., Barnes, L., Corish, C., Kennedy, N. P., Flood, P., Mulligan, S., McNamara, E., Kennedy, N. P., Flood, P., Mathias, P. M., Ball, E., Duiculescu, D., Calistru, P., O’Gorman, N., Kennedy, N. P., Abuzakouk, M., Feighery, C., Brannigan, M., Pender, S., Keeling, F., Varghese, J., Lee, M., Colreavy, M., Gaffney, R., Hone, S., Herzig, M., Walsh, M., Dolan, C., Wogan, A., Lawler, M., McCann, S. R., Hollywood, D., Donovan, D., Harmey, J., Bouchier-Hayes, D. J., Haverty, A., Wang, J. H., Harmey, J. H., Redmond, H. P., Bouchier-Hayes, D. J., McGreal, G., Shering, S. G., Moriarty, M. J., Shortt, A., Kilbane, M. T., Smith, D. F., McDermott, E. W. M., O’Higgins, N. J., Smyth, P. P. A., McNamara, D. A., Harmey, J., Wang, J. H., Donovan, D., Walsh, T. N., Bouchier-Hayes, D. J., Kay, E., Pidgeon, G., Harmey, J., McNamara, D. A., Bouchier-Hayes, D. J., Dunne, P., Lambkin, H., Russell, J. M., O’Neill, A. J., Dunne, B. M., O’Donovan, M., Lawler, M., Gaffney, E. F., Gillan, J. E., Cotter, T. G., Horan, J., Jones, D., Biswas, S. K., Mulkerrin, E. C., Brady, H., O’Donnell, J., Neary, J., Healy, E., Watson, A., Keogh, B., Ryan, M., Cassidy, C., Ward, S., Stokes, E., Keoghan, F., Barrett, A., O’Connell, P., Ryall, N., O’Connell, P. A., Jenkinson, A., O’Brien, T., O’Connell, P. G., Harrison, R., Barrett, T., Bailey, D. M. D., Butler, A., Barton, D. E., Byrne, C., McElwaine, S., McCann, S. R., Lawler, M., Cusack, S., Lawler, M., White, B., Smith, O. P., Daly, G., Gill, M., Heron, S., Hawi, Z., Fitzgerald, M., Hawi, Z., Mynett-Johnson, L., Shiels, D., Kendler, K., McKeon, P., Gill, M., Straub, R., Walsh, D., Ryan, F., Barton, D. E., McCabe, D., Murphy, R., Segurado, R., Mulcahy, T., Larson, B., Comerford, C., O’Connell, R., O’Mahony, E., Gill, M., Donnelly, J., Minahan, F., O’Neill, D., Farrell, Z., O’Neill, D., Jones, D., Horan, J., Glynn, C., Biswas, S. K., Mulkerrin, E., Brady, H., Lennox, S. E., Murphy, A., Rea, I. M., McNulty, H., McMeel, C., O’Neill, D., McEvoy, H., Freaney, R., McKenna, M. J., Crowe, M., Keating, D., Colreavy, M., Hone, S., Norman, G., Widda, S., Viani, L., Galvin, Nolan, C. M., Hardiman, O., Hardiman, O., Brett, F., Droogan, O., Gallagher, P., Harmey, M., King, M., Murphy, J., Perryrnan, R., Sukumaran, S., Walsh, J., Farrell, M. A., Hughes, G., Cunningham, C., Walsh, J. B., Coakley, D., O’Neill, D., Hurson, M., Flood, P., McMonagle, P., Hardiman, O., Ryan, F., O’Sullivan, S., Merry, C., Dodd, P., Redmond, J., Mulcahy, F. M., Browne, R., Keating, S., O’Connor, J., Cassidy, B. P., Smyth, R., Sheppard, N. P., Cullivan, R., Crown, J., Walsh, N., Denihan, A., Bruce, I., Radic, A., Coakley, D., Lawlor, B. A., Bridges, P. K., O’Doherty, M., Farrington, A., O’Doherty, M., Farragher, B., Fahy, S., Kelly, R., Carey, T., Owens, J., Gallagher, O., Sloan, D., McDonough, C., Casey, P., Horgan, A., Elneihum, A., O’Neill, C., McMonagle, T., Quinn, J., Meagher, D., Murphy, P., Kinsella, A., Mullaney, J., Waddington, J. L., Rooney, S., Rooney, S., Bamford, L., Sloan, D., O’Connor, J. J., Franklin, R., O’Brien, K., Fitzpatrick, G., Laffey, J. G., Boylan, J. F., Laffey, J., Coleman, M., Boylan, J., Laffey, J. G., McShane, A. J., Boylan, J. F., Loughrey, J. P. R., Gardiner, J., McGinley, J., Leonard, I., Carey, M., Neligan, P., O’Rourke, J., Cunningham, A., Fennessy, F., Kelly, C., Bouchier-Hayes, D., Fennessy, F., Wang, J. H., Kelly, C., Bouchier-Hayes, D., Fennessy, F., Wang, J. H., Kelly, C., Bouchier-Hayes, D. J., Kellett, J., Laffey, J., Murphy, D., Regan, J., O’Keeffe, D., Mahmud, A., Hemeryck, L., Feely, J., Mahmud, A., Hemeryck, L., Hall, M., Feely, J., Menown, I. B. A., Mathew, T. P., Nesbitt, G. S., Syme, M., Young, I. S., Adgey, A. A. J., Menown, I. B. A., Turtle, F., Allen, J., Anderson, J., Adgey, A. A. J., O’Hanlon, R., Codd, M. B., Walkin, S., McCann, H. A., Sugrue, D. D., Rasheed, A. M., Chen, G., Kelly, C., Bouchier-Hayes, D. J., Leahy, A., Rasheed, A. M., Kay, E., Jina, S., Bouchier-Hayes, D. J., Leahy, A., McDowell, I., Rasheed, A. M., Wang, J. H., Wo, Q., Kelly, C., Bouchier-Hayes, D. J., Leahy, A., Shuhaibar, M. N., McGovern, E., Turtle, F., Menown, I. B. A., Manoharan, G., Kirkpatrick, R., Campbell, N. P. S., Walkin, S., Codd, M. B., O’Hanlon, R., McCarthy, C., McCann, H. A., Sugrue, D. D., Wen, Y., Killalea, S., Hall, M., Hemeryck, L., Feely, J., Fahy, C. J., Griffith, A., McGinley, J., McCabe, D., Fraser, A., Casey, E., Ryan, T., Murphy, R., Browne, M., Fenton, J., Hughes, J., Timon, C. I., Fenton, J., Curran, A., Smyth, D., Viani, L., Walsh, M., Hughes, J. P., Fenton, J., Lee, P., Kelly, A., Timon, C. I., Hughes, J. P., Fenton, J., Shine, N., Blayney, A., McShane, D. P., Timon, C. I., Hussey, J., Howlett, M., Langton, A., McEvoy, A., Slevin, J., Fitzpatrick, C., Turner, M. J., Enright, F., Goggin, N., Costigan, C., Duff, D., Osizlok, P., Wood, F., Watson, R., Fitzsimons, R. B., Flanagan, N., Enright, F., Barnes, L., Watson, R., Molloy, E., Griffin, E., Deasy, P. F., Sheridan, M., White, M. J., Moore, R., Gray, A., Hill, J., Glasgow, J. F. T., Middleton, B., Slattery, D., Donoghue, V., McMahon, A., Murphy, J., Slattery, D., McCarthy, A., Oslislok, P., Duff, D., Colreavy, M., Keogh, I., Hone, S., Walsh, M., Henry, M., Koston, S., McMahon, K., MacNee, W., FitzGerald, M. X., O’Connor, C. M., Russell, K. J., Henry, M., Fitzgerald, M. X., O’Connor, C. M., Kavanagh, P. V., McNamara, S. M., Feely, J., Barry, M., O’Brien, J. E., McCormick, P., Molony, C., Doyle, R. M., Walsh, J. B., Coakley, D., Codd, M. B., O’Connell, P. R., Dowey, L. C., McGlynn, H., Thurnham, D. I., Elborn, S. J., Flynn, L., Carton, J., Byrne, B., O’Farrelly, C., Kelehan, P., O’Herlihy, C., O’Hara, A. M., Moran, A. P., Orren, A., Fernie, B. A., Merry, C., Clarke, S., Courtney, G., de Gascun, C., Mulcahy, F. M., Merry, C., Ryan, M., Barry, M., Mulcahy, F. M., Merry, C., Ryan, M., Barry, M., Mulcahy, F. M., Byrne, M., Moylett, E., Murphy, H., Butler, K., Nourse, C., Thaker, H., Barry, C., Russell, J., Sheehan, G., Boyle, B., Hone, R., Conboy, B., Butler, C., Moris, D., Cormican, M., Flynn, J., McCormack, O., Corbally, N., Murray, A., Kirrane, S., O’Keane, C., Hone, R., Lynch, S. M., Cryan, B., Whyte, D., Morris, D., Butler, C., Cormican, M., Flynn, J., Corbett-Feeney, G., Murray, A., Corbally, N., Hone, R., Mackle, T., Colreavy, M., Perkins, J., Saidlear, C., Young, A., Eustace, P., Wrigley, M., Clifford, J., Waddington, J. L., Tighe, O., Croke, D. T., Drago, J., Sibley, D. R., Feely, J., Kelly, A., Carvalho, M., Hennessy, M., Kelly, M., Feely, J., Hughes, C., Hanlon, M., Feely, J., Sabra, K., Keane, T., Egan, D., Ryan, M., Maerry, C., Ryan, M., Barry, M., Mulcahy, F. M., Maerry, C., Ryan, M., Barry, M., Mulcahy, F. M., Sharma, S. C., Williams, D., Kelly, A., Carvalho, M., Feely, J., Williams, D., Kelly, A., Carvalho, M., Feely, J., Codd, M. B., Mahon, N. G., McCann, H. A., Sugrue, D. D., Sayers, G. M., Johnson, Z., McNamara, S. M., Kavanagh, P. V., and Feely, J.

Published
1998
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13. Transmission of HIV drug resistance and the predicted effect on current first-line regimens in Europe

Author

Hofstra, L.M. Sauvageot, N. Albert, J. Alexiev, I. Garcia, F. Struck, D. Van De Vijver, D.A.M.C. Åsjö, B. Beshkov, D. Coughlan, S. Descamps, D. Griskevicius, A. Hamouda, O. Horban, A. Van Kasteren, M. Kolupajeva, T. Kostrikis, L.G. Liitsola, K. Linka, M. Mor, O. Nielsen, C. Otelea, D. Paraskevis, D. Paredes, R. Poljak, M. Puchhammer-Stöckl, E. Sönnerborg, A. Staneková, D. Stanojevic, M. Van Laethem, K. Zazzi, M. Lepej, S.Z. Boucher, C.A.B. Schmit, J.-C. Wensing, A.M.J. Puchhammer-Stockl, E. Sarcletti, M. Schmied, B. Geit, M. Balluch, G. Vandamme, A.-M. Vercauteren, J. Derdelinckx, I. Sasse, A. Bogaert, M. Ceunen, H. De Roo, A. De Wit, S. Echahidi, F. Fransen, K. Goffard, J.-C. Goubau, P. Goudeseune, E. Yombi, J.-C. Lacor, P. Liesnard, C. Moutschen, M. Pierard, D. Rens, R. Schrooten, Y. Vaira, D. Vandekerckhove, L.P.R. Van Den Heuvel, A. Van Der Gucht, B. Van Ranst, M. Van Wijngaerden, E. Vandercam, B. Vekemans, M. Verhofstede, C. Clumeck, N. Begovac, J. Demetriades, I. Kousiappa, I. Demetriou, V. Hezka, J. Maly, M. Machala, L. Jørgensen, L.B. Gerstoft, J. Mathiesen, L. Pedersen, C. Nielsen, H. Laursen, A. Kvinesdal, B. Ristola, M. Suni, J. Sutinen, J. Assoumou, L. Castor, G. Grude, M. Flandre, P. Storto, A. Kücherer, C. Berg, T. Braun, P. Poggensee, G. Däumer, M. Eberle, J. Heiken, H. Kaiser, R. Knechten, H. Korn, K. Müller, H. Neifer, S. Schmidt, B. Walter, H. Gunsenheimer-Bartmeyer, B. Harrer, T. Hatzakis, A. Zavitsanou, A. Vassilakis, A. Lazanas, M. Chini, M. Lioni, A. Sakka, V. Kourkounti, S. Paparizos, V. Antoniadou, A. Papadopoulos, A. Poulakou, G. Katsarolis, I. Protopapas, K. Chryssos, G. Drimis, S. Gargalianos, P. Xylomenos, G. Lourida, G. Psichogiou, M. Daikos, G.L. Sipsas, N.V. Kontos, A. Gamaletsou, M.N. Koratzanis, G. Sambatakou, E. Mariolis, H. Skoutelis, A. Papastamopoulos, V. Georgiou, O. Panagopoulos, P. Maltezos, E. De Gascun, C. Byrne, C. Duffy, M. Bergin, C. Reidy, D. Farrell, G. Lambert, J. O'Connor, E. Rochford, A. Low, J. Coakely, P. O'Dea, S. Hall, W. Levi, I. Chemtob, D. Grossman, Z. De Luca, A. Balotta, C. Riva, C. Mussini, C. Caramma, I. Capetti, A. Colombo, M.C. Rossi, C. Prati, F. Tramuto, F. Vitale, F. Ciccozzi, M. Angarano, G. Rezza, G. Vasins, O. Lipnickiene, V. Hemmer, R. Arendt, V. Michaux, C. Staub, T. Sequin-Devaux, C. Van Kessel, A. Van Bentum, P.H.M. Brinkman, K. Connell, B.J. Van Der Ende, M.E. Hoepelman, I.M. Kuipers, M. Langebeek, N. Richter, C. Santegoets, R.M.W.J. Schrijnders-Gudde, L. Schuurman, R. Van De Ven, B.J.M. Kran, A.-M.B. Ormaasen, V. Aavitsland, P. Stanczak, J.J. Stanczak, G.P. Firlag-Burkacka, E. Wiercinska-Drapalo, A. Jablonowska, E. Maolepsza, E. Leszczyszyn-Pynka, M. Szata, W. Camacho, R. Palma, C. Borges, F. Paixão, T. Duque, V. Araújo, F. Paraschiv, S. Tudor, A.M. Cernat, R. Chiriac, C. Dumitrescu, F. Prisecariu, L.J. Jevtovic, Dj. Salemovic, D. Stanekova, D. Habekova, M. Chabadová, Z. Drobkova, T. Bukovinova, P. Shunnar, A. Truska, P. Lunar, M. Babic, D. Tomazic, J. Vidmar, L. Vovko, T. Karner, P. Monge, S. Moreno, S. Del Amo, J. Asensi, V. Sirvent, J.L. De Mendoza, C. Delgado, R. Gutiérrez, F. Berenguer, J. Garcia-Bujalance, S. Stella, N. De Los Santos, I. Blanco, J.R. Dalmau, D. Rivero, M. Segura, F. Elías, M.J.P. Alvarez, M. Chueca, N. Rodríguez-Martín, C. Vidal, C. Palomares, J.C. Viciana, I. Viciana, P. Cordoba, J. Aguilera, A. Domingo, P. Galindo, M.J. Miralles, C. Del Pozo, M.A. Ribera, E. Iribarren, J.A. Ruiz, L. De La Torre, J. Vidal, F. Clotet, B. Heidarian, A. Aperia-Peipke, K. Axelsson, M. Mild, M. Karlsson, A. Thalme, A. Navér, L. Bratt, G. Blaxhult, A. Gisslén, M. Svennerholm, B. Björkman, P. Säll, C. Mellgren, Å. Lindholm, A. Kuylenstierna, N. Montelius, R. Azimi, F. Johansson, B. Carlsson, M. Johansson, E. Ljungberg, B. Ekvall, H. Strand, A. Mäkitalo, S. Öberg, S. Holmblad, P. Höfer, M. Holmberg, H. Josefson, P. Ryding, U. Bergbrant, I. SPREAD Program

Abstract

Background. Numerous studies have shown that baseline drug resistance patterns may influence the outcome of antiretroviral therapy. Therefore, guidelines recommend drug resistance testing to guide the choice of initial regimen. In addition to optimizing individual patient management, these baseline resistance data enable transmitted drug resistance (TDR) to be surveyed for public health purposes. The SPREAD program systematically collects data to gain insight into TDR occurring in Europe since 2001. Methods. Demographic, clinical, and virological data from 4140 antiretroviral-naive human immunodeficiency virus (HIV)-infected individuals from 26 countries who were newly diagnosed between 2008 and 2010 were analyzed. Evidence of TDR was defined using the WHO list for surveillance of drug resistance mutations. Prevalence of TDR was assessed over time by comparing the results to SPREAD data from 2002 to 2007. Baseline susceptibility to antiretroviral drugs was predicted using the Stanford HIVdb program version 7.0. Results. The overall prevalence of TDR did not change significantly over time and was 8.3% (95% confidence interval, 7.2%-9.5%) in 2008-2010. The most frequent indicators of TDR were nucleoside reverse transcriptase inhibitor (NRTI) mutations (4.5%), followed by nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations (2.9%) and protease inhibitor mutations (2.0%). Baseline mutations were most predictive of reduced susceptibility to initial NNRTI-based regimens: 4.5% and 6.5% of patient isolates were predicted to have resistance to regimens containing efavirenz or rilpivirine, respectively, independent of current NRTI backbones. Conclusions. Although TDR was highest for NRTIs, the impact of baseline drug resistance patterns on susceptibility was largest for NNRTIs. The prevalence of TDR assessed by epidemiological surveys does not clearly indicate to what degree susceptibility to different drug classes is affected. © The Author 2015.

Published
2016

14. Transmission of HIV Drug Resistance and the Predicted Effect on Current First-line Regimens in Europe

Author

Moutschen, M., Hofstra, Laura Marije Arije, Sauvageot, Nicolas, Albert, Jan, Alexiev, Ivailo, Garcia, Federico, Struck, Daniel, Van, de Vijver, Åsjö, Birgitta, Beshkov, Danail, Coughlan, Suzie, Descamps, Diane, Griskevicius, Algirdas, Hamouda, Osamah, Horban, Andrzej, Van Kasteren, Marjo, Kolupajeva, Tatjana, Kostrikis, Leontios G., Liitsola, Kirsi, Linka, Marek, Mor, Orna, Nielsen, Claus, Otelea, Dan, Paraskevis, Dimitrios N., Paredes, Roger, Poljak, Mario, Puchhammer-Stöckl, Elisabeth, Sönnerborg, Anders, Staneková, Danica, Stanojevic, Maja, Van Laethem, Kristel, Zazzi, Maurizio, Zidovec Lepej, Snjezana, Boucher, Charles A. B., Schmit, Jean-Claude, Wensing, Annemarie M. J., Puchhammer-Stockl, E., Sarcletti, M., Schmied, B., Geit, M., Balluch, G., Vandamme, A. M., Vercauteren, J., Derdelinckx, I., Sasse, A., Bogaert, M., Ceunen, H., De Roo, A., De Wit, S., Echahidi, F., Fransen, K., Goffard, J. -C, Goubau, P., Goudeseune, E., Yombi, J. -C, Lacor, P., Liesnard, C., Pierard, D., Rens, R., Schrooten, Y., Vaira, D., Vandekerckhove, L. P. R., Van, den Heuvel, Van, Der Gucht, Van Ranst, M., Van Wijngaerden, E., Vandercam, B., Vekemans, M., Verhofstede, C., Clumeck, N., Van Laethem, K., Lepej, S. Z., Begovac, J., Demetriades, Ioannis, Kousiappa, Ioanna, Demetriou, Victoria L., Hezka, Johana, Linka, M., Maly, M., Machala, L., Nielsen, C., Jørgensen, L. B., Gerstoft, J., Mathiesen, L., Pedersen, C., Nielsen, H., Laursen, A., Kvinesdal, B., Liitsola, K., Ristola, M., Suni, J., Sutinen, J., Descamps, D., Assoumou, L., Castor, G., Grude, M., Flandre, P., Storto, A., Hamouda, O., Kücherer, C., Berg, T., Braun, P., Poggensee, G., Däumer, M., Eberle, J., Heiken, H., Kaiser, R., Knechten, H., Korn, K., Müller, H., Neifer, S., Schmidt, B., Walter, H., Gunsenheimer-Bartmeyer, B., Harrer, T., Hatzakis, Angelos E., Zavitsanou, Assimina, Vassilakis, A., Lazanas, Marios C., Chini, Maria C., Lioni, A., Sakka, V., Kourkounti, Sofia, Paparizos, Vassilios A., Antoniadou, Anastasia C., Papadopoulos, Antonios I., Poulakou, Garyphallia G., Katsarolis, I., Protopapas, K., Chryssos, Georgios, Drimis, Stylianos, Gargalianos, Panagiotis, Xylomenos, Georgios, Lourida, G., Psichogiou, Mina A., Daikos, George L., Sipsas, N. V., Kontos, Athanasios N., Gamaletsou, M. N., Koratzanis, Georgios, Sambatakou, H., Mariolis, H., Skoutelis, A., Papastamopoulos, V., Georgiou, O., Panagopoulos, Periklis, Maltezos, E., Coughlan, S., De Gascun, C., Byrne, C., Duffy, M., Bergin, C., Reidy, D., Farrell, G., Lambert, J., O'Connor, E., Rochford, A., Low, J., Coakely, P., O'Dea, S., Hall, W., Mor, O., Levi, I., Chemtob, D., Grossman, Z., Zazzi, M., de Luca, A., Balotta, Claudia, Riva, C., Mussini, C., Caramma, I., Capetti, A., Colombo, M. C., Rossi, C., Prati, F., Tramuto, F., Vitale, F., Ciccozzi, M., Angarano, G., Rezza, G., Kolupajeva, T., Vasins, O., Griskevicius, A., Lipnickiene, V., Schmit, J. C., Struck, D., Hemmer, R., Arendt, V., Michaux, C., Staub, T., Sequin-Devaux, C., Wensing, A. M. J., Boucher, C. A. B., van, de Vijver, van Kessel, A., van Bentum, P. H. M., Brinkman, K., Connell, B. J., van, der Ende, Hoepelman, I. M., van Kasteren, M., Kuipers, M., Langebeek, N., Richter, C., Santegoets, R. M. W. J., Schrijnders-Gudde, L., Schuurman, R., van, de Ven, Kran, A. -M B., Ormaasen, V., Aavitsland, P., Horban, A., Stanczak, J. J., Stanczak, G. P., Firlag-Burkacka, E., Wiercinska-Drapalo, A., Jablonowska, E., Maolepsza, E., Leszczyszyn-Pynka, M., Szata, W., Camacho, Ricardo J., Palma, C., Borges, F., Paixão, T., Duque, V., Araújo, F., Otelea, D., Paraschiv, S., Tudor, A. M., Cernat, R., Chiriac, C., Dumitrescu, F., Prisecariu, L. J., Stanojevic, M., Jevtovic, Dj, Salemovic, D., Stanekova, D., Habekova, M., Chabadová, Z., Drobkova, T., Bukovinova, P., Shunnar, A., Truska, P., Poljak, M., Lunar, M., Babic, Dunja Z., Tomazic, J., Vidmar, L., Vovko, T., Karner, P., Garcia, F., Paredes, R., Monge, S., Moreno, S., del Amo, J., Asensi, V., Sirvent, J. L., de Mendoza, C., Delgado, R., Gutiérrez, F., Berenguer, J., Garcia-Bujalance, S., Stella, Natalia C., de, los Santos, Blanco, J. R., Dalmau, D., Rivero, M., Segura, F., Elıás, Marıá Jesús Pérez, Alvarez, M., Chueca, N., Rodríguez-Martín, C., Vidal, C., Palomares, J. C., Viciana, I., Viciana, P., Cordoba, J., Aguilera, A., Domingo, P., Galindo, M. J., Miralles, C., del Pozo, M. A., Ribera, E., Iribarren, J. A., Ruiz, L., de, la Torre, Vidal, F., Clotet, B., Heidarian, A., Aperia-Peipke, K., Axelsson, M., Mild, M., Karlsson, A., Sönnerborg, A., Thalme, A., Navér, L., Bratt, G., Blaxhult, A., Gisslén, M., Svennerholm, B., Bergbrant, I., Björkman, Per, Säll, C., Mellgren, Å., Lindholm, A., Kuylenstierna, N., Montelius, R., Azimi, F., Johansson, B., Carlsson, M., Johansson, E., Ljungberg, B., Ekvall, H., Strand, A., Mäkitalo, S., Öberg, S., Holmblad, P., Höfer, M., Holmberg, H., Josefson, P., Ryding, U., Van Kessel, A., Clinical sciences, Microbiology and Infection Control, Supporting clinical sciences, Clinicum, Department of Medicine, Virology, Cohorte de Adultos de la Red de Investigación en SIDA, Spain., SPREAD Program, [Hofstra,LM, Sauvageot,N, Struck,D, Schmit,JC ] Luxembourg Institute of Health, Luxembourg. [Hofstra,LM, Wensing,AMJ] Department of Virology, University Medical Center Utrecht, The Netherlands. [Albert,J, Sönnerborg,A] Karolinska Institute, Solna. Karolinska University Hospital, Stockholm, Sweden. [Alexiev,I, Beshkov,D] National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria. [Garcia,F] Complejo Hospitalario Universitario de Granada. Instituto de Investigación IBS Granada, Spain. [Van de Vijver,DAMC, Boucher,CAB] Erasmus MC, University Medical Center, Rotterdam, The Netherlands. [Åsjö,B] University of Bergen, Norway. [Coughlan,S] University College Dublin, Ireland. [Descamps,D] AP-HP Groupe hospitalier Bichat-Claude Bernard. IAME INSERM UMR 1137. Université Paris Diderot Sorbonne Paris Cité, Paris, France. [Griskevicius,A] Lithuanian AIDS Center, Vilnius, Lithuania. [Hamouda,O] Robert Koch Institute, Berlin, Germany. [Horban,A] Hospital of Infectious Diseases, Warsaw, Poland. [Van Kasteren,M] St Elisabeth Hospital, Tilburg, The Netherlands. [Kolupajeva,T] Infectiology Center of Latvia, Riga. [Kostrikis,LG] University of Cyprus, Nicosia. [Liitsola,K] Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland. [Linka,M] National Reference Laboratory for HIV/AIDS, National Institute of Public Health, Prague, Czech Republic. [Mor,O] National HIV Reference Laboratory, Chaim Sheba Medical Center, Tel-Hashomer, Israel. [Nielsen,C] Statens Serum Institut, Copenhagen, Denmark. [Otelea,D] National Institute for Infectious Diseases 'Prof. dr. Matei Bals', Bucharest, Romania. [Paraskevis,D] National Retrovirus Reference Center, University of Athens, Greece. [Paredes,R] IrsiCaixa Foundation, Badalona, Spain. [Poljak,M] Faculty of Medicine, Slovenian HIV/AIDS Reference Centre, University of Ljubljana, Slovenia. [Puchhammer-Stöckl,E] Medical University Vienna, Austria. [Staneková,D] Slovak Medical University, Bratislava, Slovakia. [Stanojevic,M] Faculty of Medicine, University of Belgrade, Serbia. [Van Laethem,K] Rega Institute for Medical Research, KU Leuven, Belgium. [Zazzi,M] University of Siena, Italy. [Zidovec Lepej,S] University Hospital for Infectious Diseases 'Dr. Fran Mihaljevic', Zagreb, Croatia., This work was supported by a CORE grant of Fond National de la Recherche Luxembourg (grant number C12/BM/4011111–HIV molecular epidemiology in Europe). This work has been partially supported by the European Commission (fifth framework, grant number QLK2-CT-2001-01344, sixth framework, grant number LSHP-CT-2006-518211, DynaNets grant number 233847, seventh framework, CHAIN grant number 223131), Belgium: Belgian AIDS Reference Laboratory Fund, Belgian Fonds voor Wetenschappelijk Onderzoek (grant number G.0692.14), Cyprus: Cyprus Research Promotion Foundation (grant number Health/0104/22), Denmark: Danish AIDS Foundation, France: Agence Nationale de Recherches sur le SIDA et les Hepatites Virales, Germany: Ministry of Health (grant number 1502-686-18), Ministry of Education and Research (grant number 01KI501), Italy: Fifth National Program on HIV/AIDS, Instituto Superiore di Sanità (grant numbers 40F.56 and 20D.1.6), Luxembourg: Fondation Recherche sur le SiDA and Ministry of Health, Republic of Serbia: Ministry of Education and Science (grant number 175024), Slovakia: project 'Center of Excellence of Environmental Health,' ITMS number 26240120033, based on supporting operational research and development program financed from the European Regional Development Fund, and Sweden: Swedish Research Council and Swedish Civil Contingencies Agency., APH - Health Behaviors & Chronic Diseases, Graduate School, Hofstra, LM, Sauvageot, N, Albert, J, Alexiev, I, Garcia, F, Struck, D, Van de Vijver, DA, Åsjö, B, Beshkov, D, Coughlan, S, Descamps, D, Griskevicius, A, Hamouda, O, Horban, A, Van Kasteren, M, Kolupajeva, T, Kostrikis, LG, Liitsola, K, Linka, M, Mor, O, Nielsen, C, Otelea, D, Paraskevis, D, Paredes, R, Poljak, M, Puchhammer-Stöckl, E, Sönnerborg, A, Staneková, D, Stanojevic, M, Van Laethem, K, Zazzi, M, Lepej, SZ, Boucher, CA, Schmit, JC, Wensing, AM, SPREAD program investigators, including Vitale F and Tramuto, F, Vandamme, Annemie, Vercauteren, Jurgen, Schrooten, Yoeri, Van Ranst, Marc, Van Wijngaerden, Eric, Derdelinckx, Inge, Camacho, Ricardo Jorge, Kostrikis, Leontios G. [0000-0002-5340-7109], and Paraskevis, Dimitrios [0000-0001-6167-7152]

Subjects
Male, Human immunodeficiency virus 1, Etravirine, RNA directed DNA polymerase inhibitor, darunavir, HIV Infections, Settore MED/42 - Igiene Generale E Applicata, Disciplines and Occupations::Health Occupations::Medicine::Public Health [Medical Subject Headings], Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans [Medical Subject Headings], Salud pública, genetics, Inhibidores de proteasas, Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Data Collection::Vital Statistics::Morbidity::Prevalence [Medical Subject Headings], atazanavir, media_common, transmission, Geographicals::Geographic Locations::Europe [Medical Subject Headings], 3. Good health, microbial sensitivity test, priority journal, Europe, HIV-1, antiretroviral therapy, drug resistance, HIV/AIDS, lamivudine, Reverse Transcriptase Inhibitors/pharmacology, anti human immunodeficiency virus agent, Drug, Microbiology (medical), medicine.medical_specialty, antiviral susceptibility, Phenomena and Processes::Genetic Phenomena::Genetic Variation::Mutation [Medical Subject Headings], media_common.quotation_subject, 030106 microbiology, HIV Infections/drug therapy, Chemicals and Drugs::Chemical Actions and Uses::Pharmacologic Actions::Therapeutic Uses::Anti-Infective Agents::Antiviral Agents::Anti-Retroviral Agents::Reverse Transcriptase Inhibitors [Medical Subject Headings], Microbial Sensitivity Tests, RILPIVIRINE, Article, EFAVIRENZ, 03 medical and health sciences, transmitted drug resistance, SDG 3 - Good Health and Well-being, Humans, Transmission, human, Phenomena and Processes::Physiological Phenomena::Pharmacological Phenomena::Drug Resistance [Medical Subject Headings], REVERSE-TRANSCRIPTASE INHIBITORS, Rilpivirina, INTEGRASE, MUTATIONS, abacavir, major clinical study, Virology, Infecciones por VIH, Regimen, Antiretroviral therapy, Drug resistance, Medicine (all), Infectious Diseases, chemistry, Chemicals and Drugs::Heterocyclic Compounds::Heterocyclic Compounds, 1-Ring::Oxazines::Benzoxazines [Medical Subject Headings], Mutation, 0301 basic medicine, nevirapine, Communicable diseases, Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Statistics as Topic::Confidence Intervals [Medical Subject Headings], chemistry.chemical_compound, antiviral therapy, INFECTION, Medicine and Health Sciences, Prevalence, Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Data Collection::Surveys and Questionnaires [Medical Subject Headings], Viral, Non-U.S. Gov't, Reverse-transcriptase inhibitor, antiretrovirus agent, Research Support, Non-U.S. Gov't, Human immunodeficiency virus infected patient, Middle Aged, virology, PREVALENCE, Encuestas y Cuestionarios, ANTIRETROVIRAL TREATMENT, HIV-1/drug effects, HIV Protease Inhibitors/pharmacology, Rilpivirine, Reverse Transcriptase Inhibitors, Diseases::Immune System Diseases::Immunologic Deficiency Syndromes::HIV Infections [Medical Subject Headings], Female, HIV drug resistance, medicine.drug, Adult, Human immunodeficiency virus proteinase inhibitor, Chemicals and Drugs::Organic Chemicals::Nitriles::Rilpivirine [Medical Subject Headings], Efavirenz, Anti-HIV Agents, Research Support, Resistencia a medicamentos, Settore MED/17 - MALATTIE INFETTIVE, antiviral resistance, Internal medicine, Anti-HIV Agents/pharmacology, Drug Resistance, Viral, Journal Article, medicine, Chemicals and Drugs::Chemical Actions and Uses::Pharmacologic Actions::Molecular Mechanisms of Pharmacological Action::Enzyme Inhibitors::Protease Inhibitors [Medical Subject Headings], abacavir plus lamivudine, Europa (Continente), HIV Protease Inhibitors, emtricitabine, nonhuman, Intervalos de confianza, Mutación, business.industry, HIV, prediction, Inhibidores de la transcriptasa inversa, Human immunodeficiency virus 1 infection, tenofovir, INDIVIDUALS, Drug Resistance, Viral/genetics, Benzoxazinas, ETRAVIRINE, drug effects, 3121 General medicine, internal medicine and other clinical medicine, Prevalencia, business
Abstract

Transmitted human immunodeficiency virus drug resistance in Europe is stable at around 8%. The impact of baseline mutation patterns on susceptibility to antiretroviral drugs should be addressed using clinical guidelines. The impact on baseline susceptibility is largest for nonnucleoside reverse transcriptase inhibitors., Background. Numerous studies have shown that baseline drug resistance patterns may influence the outcome of antiretroviral therapy. Therefore, guidelines recommend drug resistance testing to guide the choice of initial regimen. In addition to optimizing individual patient management, these baseline resistance data enable transmitted drug resistance (TDR) to be surveyed for public health purposes. The SPREAD program systematically collects data to gain insight into TDR occurring in Europe since 2001. Methods. Demographic, clinical, and virological data from 4140 antiretroviral-naive human immunodeficiency virus (HIV)–infected individuals from 26 countries who were newly diagnosed between 2008 and 2010 were analyzed. Evidence of TDR was defined using the WHO list for surveillance of drug resistance mutations. Prevalence of TDR was assessed over time by comparing the results to SPREAD data from 2002 to 2007. Baseline susceptibility to antiretroviral drugs was predicted using the Stanford HIVdb program version 7.0. Results. The overall prevalence of TDR did not change significantly over time and was 8.3% (95% confidence interval, 7.2%–9.5%) in 2008–2010. The most frequent indicators of TDR were nucleoside reverse transcriptase inhibitor (NRTI) mutations (4.5%), followed by nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations (2.9%) and protease inhibitor mutations (2.0%). Baseline mutations were most predictive of reduced susceptibility to initial NNRTI-based regimens: 4.5% and 6.5% of patient isolates were predicted to have resistance to regimens containing efavirenz or rilpivirine, respectively, independent of current NRTI backbones. Conclusions. Although TDR was highest for NRTIs, the impact of baseline drug resistance patterns on susceptibility was largest for NNRTIs. The prevalence of TDR assessed by epidemiological surveys does not clearly indicate to what degree susceptibility to different drug classes is affected.

Published
2016
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18. Increase in transmitted resistance to non-nucleoside reverse transcriptase inhibitors among newly diagnosed HIV-1 infections in Europe

Author

Frentz, D. Van de Vijver, D.A.M.C. Abecasis, A.B. Albert, J. Hamouda, O. Jørgensen, L.B. Kücherer, C. Struck, D. Schmit, J.-C. Vercauteren, J. Åsjö, B. Balotta, C. Beshkov, D. Camacho, R.J. Clotet, B. Coughlan, S. Griskevicius, A. Grossman, Z. Horban, A. Kolupajeva, T. Korn, K. Kostrikis, L.G. Liitsola, K. Linka, M. Nielsen, C. Otelea, D. Paraskevis, D. Paredes, R. Poljak, M. Puchhammer-Stöckl, E. Sönnerborg, A. Stanekova, D. Stanojevic, M. Van Wijngaerden, E. Wensing, A.M.J. Boucher, C.A.B. Puchhammer-Stockl, E. Sarcletti, M. Schmied, B. Geit, M. Balluch, G. Vandamme, A.-M. Vercauteren, J. Derdelinckx, I. Sasse, A. Bogaert, M. Ceunen, H. De Roo, A. De Wit, S. Echahidi, F. Fransen, K. Goffard, J.-C. Goubau, P. Goudeseune, E. Yombi, J.-C. Lacor, P. Liesnard, C. Moutschen, M. Pierard, D. Rens, R. Schrooten, Y. Vaira, D. Vandekerckhove, L.P.R. Van den Heuvel, A. Van Der Gucht, B. Van Ranst, M. Vandercam, B. Vekemans, M. Verhofstede, C. Clumeck, N. Van Laethem, K. Demetriades, I. Kousiappa, I. Demetriou, V. Hezka, J. Bruckova, M. Linka, M. Machala, L. Nielsen, C. Jørgensen, L.B. Gerstoft, J. Mathiesen, L. Pedersen, C. Nielsen, H. Laursen, A. Kvinesdal, B. Salminen, M. Ristola, M. Liitsola, K. Suni, J. Sutinen, J. Korn, K. Kücherer, C. Berg, T. Braun, P. Poggensee, G. Däumer, M. Eberle, J. Heiken, H. Kaiser, R. Knechten, H. Müller, H. Neifer, S. Schmidt, B. Walter, H. Gunsenheimer-Bartmeyer, B. Harrer, T. Paraskevis, D. Hatzakis, A. Magiorkinis, E. Hatzitheodorou, E. Haida, C. Zavitsanou, A. Magiorkinis, G. Lazanas, M. Chini, M. Magafas, N. Tsogas, N. Paparizos, V. Kourkounti, S. Antoniadou, A. Papadopoulos, A. Panagopoulos, P. Poulakou, G. Sakka, V. Chryssos, G. Drimis, S. Gargalianos, P. Lelekis, M. Chilomenos, G. Psichogiou, M. Daikos, G.L. Panos, G. Haratsis, G. Kordossis, T. Kontos, A. Koratzanis, G. Theodoridou, M. Mostrou, G. Spoulou, V. Coughlan, S. De Gascun, C. Byrne, C. Duffy, M. Bergin, C. Reidy, D. Farrell, G. Lambert, J. O'Connor, E. Rochford, A. Low, J. Coakely, P. O'Dea, S. Hall, W. Grossman, Z. Levi, I. Chemtob, D. Balotta, C. Riva, C. Mussini, C. Caramma, I. Capetti, A. Colombo, M.C. Rossi, C. Prati, F. Tramuto, F. Vitale, F. Ciccozzi, M. Angarano, G. Rezza, G. Schmit, J.C. Struck, D. Hemmer, R. Arendt, V. Staub, T. Schneider, F. Roman, F. Wensing, A.M.J. Boucher, C.A.B. van Kessel, A. van Bentum, P.H.M. Brinkman, K. op de Coul, E.L. van der Ende, M.E. Hoepelman, I. van Kasteren, M. Juttmann, J. Kuipers, M. Langebeek, N. Richter, C. Santegoets, R. Schrijnders-Gudde, L. Schuurman, R. van de Ven, B.J.M. Åsjö, B. Ormaasen, V. Aavitsland, P. Horban, A. Stanczak, J.J. Stanczak, G.P. Firlag-Burkacka, E. Wiercinska-Drapalo, A. Jablonowska, E. Malolepsza, E. Leszczyszyn-Pynka, M. Szata, W. Camacho, R. Palma, C. Borges, F. Paixão, T. Duque, V. Araújo, F. Jevtovic, D. Salemovic, D. Stanekova, D. Habekova, M. Mokras, M. Truska, P. Poljak, M. Lunar, M. Babic, D. Tomazic, J. Vidmar, L. Vovko, T. Karner, P. Clotet, B. Domingo, P. Galindo, M.J. Miralles, C. del Pozo, M.A. Ribera, E. Iribarren, J.A. Ruiz, L. de la Torre, J. Vidal, F. Garcia, F. Paredes, R. Albert, J. Heidarian, A. Aperia-Peipke, K. Axelsson, M. Mild, M. Karlsson, A. Sönnerborg, A. Thalme, A. Navér, L. Bratt, G. Karlsson, A. Blaxhult, A. Gisslén, M. Svennerholm, B. Bergbrant, I. Björkman, P. Säll, C. Mellgren, Å. Lindholm, A. Kuylenstierna, N. Montelius, R. Azimi, F. Johansson, B. Carlsson, M. Johansson, E. Ljungberg, B. Ekvall, H. Strand, A. Mäkitalo, S. öberg, S. Holmblad, P. Höfer, M. Holmberg, H. Josefson, P. Ryding, U. on behalf of the SPREAD Programme

Abstract

Background: One out of ten newly diagnosed patients in Europe was infected with a virus carrying a drug resistant mutation. We analysed the patterns over time for transmitted drug resistance mutations (TDRM) using data from the European Spread program.Methods: Clinical, epidemiological and virological data from 4317 patients newly diagnosed with HIV-1 infection between 2002 and 2007 were analysed. Patients were enrolled using a pre-defined sampling strategy.Results: The overall prevalence of TDRM in this period was 8.9% (95% CI: 8.1-9.8). Interestingly, significant changes over time in TDRM caused by the different drug classes were found. Whereas nucleoside resistance mutations remained constant at 5%, a significant decline in protease inhibitors resistance mutations was observed, from 3.9% in 2002 to 1.6% in 2007 (p = 0.001). In contrast, resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) doubled from 2.0% in 2002 to 4.1% in 2007 (p = 0.004) with 58% of viral strains carrying a K103N mutation. Phylogenetic analysis showed that these temporal changes could not be explained by large clusters of TDRM.Conclusion: During the years 2002 to 2007 transmitted resistance to NNRTI has doubled to 4% in Europe. The frequent use of NNRTI in first-line regimens and the clinical impact of NNRTI mutations warrants continued monitoring. © 2014 Frentz et al.; licensee BioMed Central Ltd.

Published
2014

19. Limited cross-border infections in patients newly diagnosed with HIV in Europe

Author

Moutschen, M., Frentz, D., Wensing, A. M. J., Albert, Jan, Paraskevis, Dimitrios N., Abecasis, A. B., Hamouda, O., Jørgensen, L. B., Kücherer, C., Struck, D., Schmit, J. -C, Åsjö, Birgitta, Balotta, Claudia, Beshkov, Danail, Camacho, Ricardo J., Clotet, B., Coughlan, S., De Wit, S., Griskevicius, A., Grossman, Z., Horban, A., Kolupajeva, T., Korn, K., Kostrikis, Leontios G., Liitsola, K., Linka, M., Nielsen, C., Otelea, D., Paredes, R., Poljak, M., Puchhammer-Stöckl, E., Sönnerborg, A., Stanekova, D., Stanojevic, M., Vandamme, A. -M, Boucher, C. A. B., Van de Vijver, D. A. M. C., Balluch, G., Vercauteren, J., Derdelinckx, I., Sasse, A., Bogaert, M., Ceunen, H., De Roo, A., Echahidi, F., Fransen, K., Goffard, J. -C, Goubau, P., Goudeseune, E., Yombi, J. -C, Lacor, P., Liesnard, C., Pierard, D., Rens, R., Schrooten, Y., Vaira, D., Vandekerckhove, L. P. R., Van den Heuvel, A., Van Der Gucht, B., Van Ranst, M., Van Wijngaerden, E., Vandercam, B., Vekemans, M., Verhofstede, C., Clumeck, N., Van Laethem, K., Demetriades, Ioannis, Kousiappa, Ioanna, Demetriou, Victoria L., Hezka, Johana, Bruckova, M., Machala, L., Gerstoft, J., Mathiesen, L., Pedersen, C., Nielsen, H., Laursen, A., Kvinesdal, B., Salminen, M., Ristola, M., Suni, J., Sutinen, J., Berg, T., Braun, P., Poggensee, G., Däumer, M., Eberle, J., Heiken, H., Kaiser, R., Knechten, H., Müller, H., Neifer, S., Schmidt, B., Walter, H., Gunsenheimer-Bartmeyer, B., Harrer, T., Hatzakis, Angelos E., Magiorkinis, Emmanouil N., Hatzitheodorou, Eleni, Haida, Catherine, Zavitsanou, Assimina, Magiorkinis, Gkikas, Lazanas, Marios C., Chini, Maria C., Magafas, N., Tsogas, Nickolaos, Paparizos, Vassilios A., Kourkounti, Sofia, Antoniadou, Anastasia C., Papadopoulos, Antonios I., Panagopoulos, Periklis, Poulakou, Garyphallia G., Sakka, V., Chryssos, Georgios, Drimis, Stylianos, Gargalianos, Panagiotis, Lelekis, Moyssis I., Chilomenos, G., Psichogiou, Mina A., Daikos, George L., Panos, George, Haratsis, G., Kordossis, Theodore, Kontos, Athanasios N., Koratzanis, Georgios, Theodoridou, Maria C., Mostrou, Glykeria J., Spoulou, Vana I., De Gascun, C., Byrne, C., Duffy, M., Bergin, C., Reidy, D., Farrell, G., Lambert, J., O'Connor, E., Rochford, A., Low, J., Coakely, P., O'Dea, S., Hall, W., Levi, I., Chemtob, D., Franzetti, M., Lai, A., Binda, F., Tramuto, F., Ciccozzi, M., Mussini, C., Angarano, G., Rezza, G., Schmit, J. C., Hemmer, R., Arendt, V., Staub, T., Schneider, F., Roman, F., van Kessel, A., van Bentum, P. H. M., Brinkman, K., de Coul, E. L., van der Ende, M. E., Hoepelman, I. M., van Kasteren, M., Juttmann, J., Kuipers, M., Langebeek, N., Richter, C., Santegoets, R. M. W. J., Schrijnders-Gudde, L., Schuurman, R., van de Ven, B. J. M., Ormaasen, V., Aavitsland, P., Stanczak, J. J., Stanczak, G. P., Firlag-Burkacka, E., Wiercinska-Drapalo, A., Jablonowska, E., Malolepsza, E., Leszczyszyn-Pynka, M., Szata, W., Palma, C., Borges, F., Paixão, T., Duque, V., Araújo, F., Jevtovic, D., Salemovic, D., Habekova, M., Mokráš, Miloš, Truska, P., Lunar, M., Babic, Dunja Z., Tomazic, J., Vidmar, L., Vovko, T., Karner, P., Domingo, P., Galindo, M. J., Miralles, C., del Pozo, M. A., Ribera, E., Iribarren, J. A., Ruiz, L., de la Torre, J., Vidal, F., Garcia, F., Heidarian, A., Aperia-Peipke, K., Axelsson, M., Mild, M., Karlsson, A., Thalme, A., Navér, L., Bratt, G., Blaxhult, A., Gisslén, M., Svennerholm, B., Bergbrant, I., Björkman, Per, Säll, C., Mellgren, Å., Lindholm, A., Kuylenstierna, N., Montelius, R., Azimi, F., Johansson, B., Carlsson, M., Johansson, E., Ljungberg, B., Ekvall, H., Strand, A., Mäkitalo, S., öberg, S., Holmblad, P., Höfer, M., Holmberg, H., Josefson, P., Ryding, U., Van Kessel, A., Instituto de Higiene e Medicina Tropical (IHMT), Centro de Malária e outras Doenças Tropicais (CMDT), Clinicum, Department of Medicine, Infektiosairauksien yksikkö, Frentz, D, Wensing, AMJ, Albert, J, Paraskevis, D, Abecasis, AB, Hamouda, O, Jørgensen, LB, Kücherer, C, Struck, D, Schmit, JC, Åsjö, B, Balotta, C, Beshkov, D, Camacho, RJ, Clotet, B, Coughlan, S, De Wit, S, Griskevicius, A, Grossman, Z, Horban, A, Kolupajeva, T, Korn, K, Kostrikis, LG, Liitsola, K, Linka, M, Nielsen, C, Otelea, D, Paredes, R, Poljak, M, Puchhammer-Stöckl, E, Sönnerborg, A, Stanekova, D, Stanojevic, M, Vandamme, AM, Boucher, CAB, Van de Vijver, DAMC, Tramuto, F, Van Wijngaerden, Eric, Van Ranst, Marc, Van Laethem, Kristel, Derdelinckx, Inge, Kostrikis, Leontios G. [0000-0002-5340-7109], Paraskevis, Dimitrios [0000-0001-6167-7152], Virology, and Graduate School

Subjects
Male, Epidemiology, Human immunodeficiency virus (HIV), Human immunodeficiency virus 1, HIV Infections, medicine.disease_cause, Virologie générale, phylogeny, Settore MED/42 - Igiene Generale E Applicata, Men who have sex with men, EMERGENCE, 0302 clinical medicine, Medicine and Health Sciences, Medicine, Infection control, Cluster Analysis, 030212 general & internal medicine, Israel, Pathologie maladies infectieuses, travel, Phylogeny, 0303 health sciences, Molecular Epidemiology, Travel, Transmission (medicine), article, virus transmission, IMMUNODEFICIENCY-VIRUS TYPE-1, 3. Good health, Europe, female, Infectious Diseases, SUBTYPE B, DRUG-RESISTANT HIV-1, RNA, Viral, male homosexual, Adult, structural gene, Molecular Sequence Data, Newly diagnosed, Clusters, 03 medical and health sciences, male, SDG 3 - Good Health and Well-being, MOLECULAR EPIDEMIOLOGY, SWITZERLAND, Virology, geographic distribution, Humans, Transmission, In patient, human, 030304 developmental biology, nonhuman, Molecular epidemiology, business.industry, Research, high risk population, Virologie médicale, nucleotide sequence, Sequence Analysis, DNA, Human immunodeficiency virus 1 infection, major clinical study, unindexed sequence, 3121 General medicine, internal medicine and other clinical medicine, HIV-1, business, Europe, HIV-1, Transmission, Clusters, Demography, cluster analysis
Abstract

Background: International travel plays a role in the spread of HIV-1 across Europe. It is, however, not known whether international travel is more important for spread of the epidemic as compared to endogenous infections within single countries. In this study, phylogenetic associations among HIV of newly diagnosed patients were determined across Europe.Results: Data came from the SPREAD programme which collects samples of newly diagnosed patients that are representative for national HIV epidemics. 4260 pol sequences from 25 European countries and Israel collected in 2002-2007 were included.We identified 457 clusters including 1330 persons (31.2% of all patients). The cluster size ranged between 2 and 28. A number of 987 patients (74.2%) were part of a cluster that consisted only of patients originating from the same country. In addition, 135 patients (10.2%) were in a cluster including only individuals from neighboring countries. Finally, 208 patients (15.6%) clustered with individuals from countries without a common border. Clustering with patients from the same country was less prevalent in patients being infected with B subtype (P-value, SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2013

20. Transfusion‐transmitted hepatitis B virus (HBV) infection from an individual‐donation nucleic acid (ID‐NAT) non‐reactive donor.

Author

O'Flaherty, N., Ushiro‐Lumb, I., Pomeroy, L., Ijaz, S., Boland, F., De Gascun, C., Fitzgerald, J., and O'Riordan, J.

Subjects
BLOOD transfusion reaction, HEPATITIS B virus, BLOOD donors, NUCLEIC acids, IMMUNOCOMPROMISED patients
Abstract

Lookback was initiated upon notification of an acute HBV infection in a repeat Irish donor, 108 days post‐donation. The donation screened non‐reactive by individual‐donation nucleic acid testing (ID‐NAT) using the Procleix Ultrio Elite multiplex assay and again when the archived sample was retested, but the discriminatory assay for HBV was reactive. The immunocompromised recipient of the implicated red cell component was tested 110 days post‐transfusion, revealing a HBV DNA viral load of 470 IU/ml. Genotype C2 sequences identical across two regions of the HBV genome were found in samples from the donor and recipient. [ABSTRACT FROM AUTHOR]

Published
2018
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21. HIV-1 subtype distribution and its demographic determinants in newly diagnosed patients in Europe suggest highly compartmentalized epidemics

Author

Abecasis, A.B. Wensing, A.M.J. Paraskevis, D. Vercauteren, J. Theys, K. Van de Vijver, D.A.M.C. Albert, J. Asjö, B. Balotta, C. Beshkov, D. Camacho, R.J. Clotet, B. De Gascun, C. Griskevicius, A. Grossman, Z. Hamouda, O. Horban, A. Kolupajeva, T. Korn, K. Kostrikis, L.G. Kücherer, C. Liitsola, K. Linka, M. Nielsen, C. Otelea, D. Paredes, R. Poljak, M. Puchhammer-Stöckl, E. Schmit, J.-C. Sönnerborg, A. Stanekova, D. Stanojevic, M. Struck, D. Boucher, C.A.B. Vandamme, A.-M.

Abstract

Background: Understanding HIV-1 subtype distribution and epidemiology can assist preventive measures and clinical decisions. Sequence variation may affect antiviral drug resistance development, disease progression, evolutionary rates and transmission routes.Results: We investigated the subtype distribution of HIV-1 in Europe and Israel in a representative sample of patients diagnosed between 2002 and 2005 and related it to the demographic data available. 2793 PRO-RT sequences were subtyped either with the REGA Subtyping tool or by a manual procedure that included phylogenetic tree and recombination analysis. The most prevalent subtypes/CRFs in our dataset were subtype B (66.1%), followed by sub-subtype A1 (6.9%), subtype C (6.8%) and CRF02_AG (4.7%). Substantial differences in the proportion of new diagnoses with distinct subtypes were found between European countries: the lowest proportion of subtype B was found in Israel (27.9%) and Portugal (39.2%), while the highest was observed in Poland (96.2%) and Slovenia (93.6%). Other subtypes were significantly more diagnosed in immigrant populations. Subtype B was significantly more diagnosed in men than in women and in MSM > IDUs > heterosexuals. Furthermore, the subtype distribution according to continent of origin of the patients suggests they acquired their infection there or in Europe from compatriots.Conclusions: The association of subtype with demographic parameters suggests highly compartmentalized epidemics, determined by social and behavioural characteristics of the patients. © 2013 Abecasis et al.; licensee BioMed Central Ltd.

Published
2013

22. Treatment-associated polymorphisms in protease are significantly associated with higher viral load and lower CD4 count in newly diagnosed drug-naive HIV-1 infected patients

Author

Moutschen, M., Theys, K., Deforche, K., Vercauteren, J., Libin, P., van de Vijver, D. A. M. C., Albert, Jan, Åsjö, Birgitta, Balotta, Claudia, Bruckova, M., Camacho, Ricardo J., Clotet, B., Coughlan, S., Grossman, Z., Hamouda, O., Horban, A., Korn, K., Kostrikis, Leontios G., Kücherer, C., Nielsen, C., Paraskevis, Dimitrios N., Poljak, M., Puchhammer-Stockl, E., Riva, C., Ruiz, L., Liitsola, K., Schmit, J. -C, Schuurman, R., Sönnerborg, A., Stanekova, D., Stanojevic, M., Struck, D., Van Laethem, K., Wensing, A. M. J., Boucher, C. A. B., Vandamme, A. M., Sarcletti, M., Schmied, B., Geit, M., Balluch, G., Derdelinckx, I., Sasse, A., Bogaert, M., Ceunen, H., De Roo, A., De Wit, S., Echahidi, F., Fransen, K., Goffard, J. -C, Goubau, P., Goudeseune, E., Yombi, J. -C, Lacor, P., Liesnard, C., Pierard, D., Rens, R., Schrooten, Y., Vaira, D., Van den Heuvel, A., Van Der Gucht, B., Van Ranst, M., Van Wijngaerden, E., Vandercam, B., Vekemans, M., Verhofstede, C., Clumeck, N., Demetriades, Ioannis, Kousiappa, Ioanna, Demetriou, Victoria L., Hezka, Johana, Linka, M., Machala, L., Jrgensen, L. B., Gerstoft, J., Mathiesen, L., Pedersen, C., Nielsen, H., Laursen, A., Kvinesdal, B., Ristola, M., Suni, J., Sutinen, J., K̈ucherer, C., Berg, T., Braun, P., Poggensee, G., Däumer, M., Eberle, J., Heiken, H., Kaiser, R., Knechten, H., Müller, H., Neifer, S., Schmidt, B., Walter, H., Gunsenheimer-Bartmeyer, B., Harrer, T., Hatzakis, Angelos E., Magiorkinis, Emmanouil N., Hatzitheodorou, Eleni, Issaris, C., Haida, Catherine, Zavitsanou, Assimina, Magiorkinis, Gkikas, Lazanas, Marios C., Chini, Maria C., Magafas, N., Tsogas, Nickolaos, Paparizos, Vassilios A., Kourkounti, Sofia, Antoniadou, Anastasia C., Papadopoulos, Antonios I., Panagopoulos, Periklis, Poulakou, Garyphallia G., Sakka, V., Chryssos, Georgios, Drimis, Stylianos, Gargalianos, Panagiotis, Lelekis, Moyssis I., Xilomenos, G., Psichogiou, Mina A., Daikos, George L., Panos, George, Haratsis, G., Kordossis, Theodore, Kontos, Athanasios N., Koratzanis, Georgios, Theodoridou, Maria C., Mostrou, Glykeria J., Spoulou, Vana I., Hall, W., De Gascun, C., Byrne, C., Duffy, M., Bergin, C., Reidy, D., Farrell, G., Lambert, J., O'Connor, E., Rochford, A., Low, J., Coakely, P., Levi, I., Chemtob, D., Mussini, C., Caramma, I., Capetti, A., Colombo, M. C., Rossi, C., Prati, F., Tramuto, F., Vitale, F., Ciccozzi, M., Angarano, G., Rezza, G., Schmit, J. C., Hemmer, R., Arendt, V., Staub, T., Schneider, F., Roman, F., van Bentum, P. H. M., Brinkman, K., op de Coul, E. L., van der Ende, M. E., Hoepelman, I. M., van Kasteren, M., Juttmann, J., Kuipers, M., Langebeek, N., Richter, C., Santegoets, R. M. W. J., Schrijnders-Gudde, L., van de Ven, B. J. M., Ormaasen, V., Aavitsland, P., Stanczak, J. J., Stanczak, G. P., Firlag-Burkacka, E., Wiercinska-Drapalo, A., Jablonowska, E., Malolepsza, E., Leszczyszyn-Pynka, M., Szata, W., Palma, C., Borges, F., Paix̃ao, T., Duque, V., Araújo, F., Jevtovic, D. J., Salemovic, D., Habekova, M., Mokráš, Miloš, Truska, P., Babic, Dunja Z., Tomazic, J., Vidmar, L., Karner, P., Gutíerrez, C., deMendoza, C., Erkicia, I., Domingo, P., Camino, X., Galindo, M. J., Blanco, J. L., Leal, M., Masabeu, A., Guelar, A., Llibre, J. M., Margall, N., Iribarren, J. A., Gutierrez, S., Baldov́i, J. F., Pedreira, J. D., Gatell, J. M., Moreno, S., de Mendoza, C., Soriano, V., Blaxhult, A., Heidarian, A., Karlsson, A., Aperia-Peipke, K., Bergbrant, I. -M, Gissĺen, M., Svennerholm, M., Björkman, Per, Bratt, G., Carlsson, M., Ekvall, H., Ericsson, M., Ḧofer, M., Johansson, B., Sonnerb̈org, A., Kuylenstierna, N., Ljungberg, B., Mäkitalo, S., Strand, A., Öberg, S., Virology, Erasmus MC other, Van Wijngaerden, Eric, Clinicum, Department of Medicine, Infektiosairauksien yksikkö, Centro de Malária e outras Doenças Tropicais (CMDT), Graduate School, Kostrikis, Leontios G. [0000-0002-5340-7109], Paraskevis, Dimitrios [0000-0001-6167-7152], UCL - SSS/IREC/MBLG - Pôle de Microbiologie médicale, UCL - (SLuc) Service de microbiologie, UCL - (SLuc) Service de médecine interne générale, Theys, K, Deforche, K, Vercauteren, J, Libin, P, van de Vijver, DA, Albert, J, Asjö, B, Balotta, C, Bruckova, M, Camacho, RJ, Clotet, B, Coughlan, S, Grossman, Z, Hamouda, O, Horban, A, Korn, K, Kostrikis, LG, Kücherer, C, Nielsen, C, Paraskevis, D, Poljak, M, Puchhammer Stockl, E, Riva, C, Ruiz, L, Liitsola, K, Schmit, JC, Schuurman, R, Sönnerborg, A, Stanekova, D, Stanojevic, M, Struck, D, Van Laethem, K, Wensing, AM, Boucher, CA, Vandamme, AM, Tramuto, F, and Vitale, F

Subjects
Adult, Male, lcsh:Immunologic diseases. Allergy, Anti-HIV Agents, education, Virulence, HIV Infections, Drug resistance, Biology, Settore MED/42 - Igiene Generale E Applicata, Virus, polymorphism, 03 medical and health sciences, Viral Proteins, SDG 3 - Good Health and Well-being, Virology, Genotype, Drug Resistance, Viral, drug-naive, medicine, Humans, Prospective Studies, 030304 developmental biology, 0303 health sciences, Polymorphism, Genetic, 030306 microbiology, Research, protease, Viral Load, Reverse transcriptase, 3. Good health, CD4 Lymphocyte Count, Drug-naïve, Infectious Diseases, 3121 General medicine, internal medicine and other clinical medicine, Immunology, biology.protein, HIV-1, Female, Antibody, lcsh:RC581-607, Viral load, HIV-1 infected patient, medicine.drug, Peptide Hydrolases
Abstract

Background: The effect of drug resistance transmission on disease progression in the newly infected patient is not well understood. Major drug resistance mutations severely impair viral fitness in a drug free environment, and therefore expected to revert quickly. Compensatory mutations, often already polymorphic in wild-type viruses, do not tend to revert after transmission. While compensatory mutations increase fitness during treatment, their presence may also modulate viral fitness and virulence in absence of therapy and major resistance mutations. We previously designed a modeling technique that quantifies genotypic footprints of in vivo treatment selective pressure, including both drug resistance mutations and polymorphic compensatory mutations, through the quantitative description of a fitness landscape from virus genetic sequences. Results: Genotypic correlates of viral load and CD4 cell count were evaluated in subtype B sequences from recently diagnosed treatment-naive patients enrolled in the SPREAD programme. The association of surveillance drug resistance mutations, reported compensatory mutations and fitness estimated from drug selective pressure fitness landscapes with baseline viral load and CD4 cell count was evaluated using regression techniques. Protease genotypic variability estimated to increase fitness during treatment was associated with higher viral load and lower CD4 cell counts also in treatment-naive patients, which could primarily be attributed to well-known compensatory mutations at highly polymorphic positions. By contrast, treatment-related mutations in reverse transcriptase could not explain viral load or CD4 cell count variability. Conclusions: These results suggest that polymorphic compensatory mutations in protease, reported to be selected during treatment, may improve the replicative capacity of HIV-1 even in absence of drug selective pressure or major resistance mutations. The presence of this polymorphic variation may either reflect a history of drug selective pressure, i.e. transmission from a treated patient, or merely be a result of diversity in wild-type virus. Our findings suggest that transmitted drug resistance has the potential to contribute to faster disease progression in the newly infected host and to shape the HIV-1 epidemic at a population level. ispartof: Retrovirology vol:9 issue:1 ispartof: location:England status: published

Published
2012

27. HIV-1 subtype distribution and its demographic determinants in newly diagnosed patients in Europe suggest highly compartmentalized epidemics

Author

Abecasis, A. B., Wensing, A. M. J., Paraskevis, Dimitrios N., Vercauteren, J., Theys, K., Van de Vijver, D. A. M. C., Albert, Jan, Åsjö, Birgitta, Balotta, Claudia, Beshkov, Danail, Camacho, Ricardo J., Clotet, B., De Gascun, C., Griskevicius, A., Grossman, Z., Hamouda, O., Horban, A., Kolupajeva, T., Korn, K., Kostrikis, Leontios G., Kücherer, C., Liitsola, K., Linka, M., Nielsen, C., Otelea, D., Paredes, R., Poljak, M., Puchhammer-Stöckl, E., Schmit, J. -C, Sönnerborg, A., Stanekova, D., Stanojevic, M., Struck, D., Boucher, C. A. B., Vandamme, A. -M, Virology, and Paraskevis, Dimitrios [0000-0001-6167-7152]

Subjects
Male, demography, Slovenia, Human immunodeficiency virus (HIV), Human immunodeficiency virus 1, Distribution (economics), HIV Infections, medicine.disease_cause, molecular epidemiology, epidemic, Risk Factors, computer program, Epidemiology, Israel, cladistics, genetic recombination, 0303 health sciences, Phylogenetic tree, Transmission (medicine), adult, article, homosexuality, virus transmission, Subtyping, 3. Good health, Europe, female, Infectious Diseases, virus typing, Female, lcsh:Immunologic diseases. Allergy, medicine.medical_specialty, sex difference, intravenous drug abuse, immigrant, Newly diagnosed, Biology, 03 medical and health sciences, Risk-Taking, male, SDG 3 - Good Health and Well-being, Virology, medicine, Humans, human, phylogenetic tree, Social Behavior, Epidemics, 030304 developmental biology, Portugal, 030306 microbiology, business.industry, Research, Disease progression, heterosexuality, Bayes Theorem, Human immunodeficiency virus 1 infection, major clinical study, amino acid sequence, Socioeconomic Factors, HIV-1, Human medicine, Poland, lcsh:RC581-607, business, Demography
Abstract

Background: Understanding HIV-1 subtype distribution and epidemiology can assist preventive measures and clinical decisions. Sequence variation may affect antiviral drug resistance development, disease progression, evolutionary rates and transmission routes.Results: We investigated the subtype distribution of HIV-1 in Europe and Israel in a representative sample of patients diagnosed between 2002 and 2005 and related it to the demographic data available. 2793 PRO-RT sequences were subtyped either with the REGA Subtyping tool or by a manual procedure that included phylogenetic tree and recombination analysis. The most prevalent subtypes/CRFs in our dataset were subtype B (66.1%), followed by sub-subtype A1 (6.9%), subtype C (6.8%) and CRF02_AG (4.7%). Substantial differences in the proportion of new diagnoses with distinct subtypes were found between European countries: the lowest proportion of subtype B was found in Israel (27.9%) and Portugal (39.2%), while the highest was observed in Poland (96.2%) and Slovenia (93.6%). Other subtypes were significantly more diagnosed in immigrant populations. Subtype B was significantly more diagnosed in men than in women and in MSM > IDUs > heterosexuals. Furthermore, the subtype distribution according to continent of origin of the patients suggests they acquired their infection there or in Europe from compatriots.Conclusions: The association of subtype with demographic parameters suggests highly compartmentalized epidemics, determined by social and behavioural characteristics of the patients. © 2013 Abecasis et al. licensee BioMed Central Ltd. 10 Tradenames: REGA Subtyping Cited By :55

Published
2013
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34. Torque Teno Virus Loads as a Marker of Immunosuppression in Pediatric Kidney Transplant Recipients.

Author

Kelly E, Awan A, Sweeney C, Wildes D, De Gascun C, Hassan J, and Riordan M

Subjects
Humans, Child, Transplant Recipients, Torque teno virus, Kidney Transplantation, Viral Load, DNA Virus Infections immunology, Biomarkers blood, Immunosuppressive Agents therapeutic use, Immunosuppression Therapy methods, Graft Rejection immunology, Graft Rejection prevention & control
Abstract

Background: Long-term renal function and survival after kidney transplantation rely on appropriate immunosuppressive treatment to prevent the risk of rejection. New biomarkers are needed to accurately assess the degree of immunosuppression in renal transplant recipients in order to avoid organ rejection and the development of opportunistic infections. Highly prevalent in humans, torque teno virus (TTV), which belongs to the family Anelloviridae, is a small, nonenveloped, single-stranded DNA virus which has not been linked with any specific human illness, but which constitutes a major component of the human virome. Host antiviral responses allow TTV levels to be controlled; however, viral persistence remains, explaining the high prevalence in human populations, including healthy individuals. Important confounders of TTV load include time since transplantation, age, gender, obesity, and smoking status., Aims: TTV-based guidance of immunosuppressive drug dosing could help with risk stratification, reducing the risk of infection, graft rejection and oncologic disease on an individual level, enabling long-term patient and graft survival., Methods: Original studies were accessed by a systematic search from electronic databases including PubMed, ScienceDirect and Wiley Online Library., Results: The presented data mainly derive from adult transplant recipients showing an association between TTV plasma levels and the immune status of the host: High-TTV load and high immunosuppression are associated with a risk of infection, and low-TTV load and low immunosuppression indicate a risk of rejection. However, there is minimal information on pediatric transplant recipients with further research required in this cohort. To date, it has been demonstrated that longer posttransplant times are significantly associated with lower TTV levels in children with renal transplant. Meanwhile, an association between lower TTV loads and increased risk of graft reject during the first year of transplantation was also reported. More recently, Eibensteiner et al. revealed a robust, independent association between TTV plasma load and the onset of Cytomegalovirus and BK virus infections., Conclusion: Data from randomized controlled trials are still missing, even in adults, but a multicenter randomized controlled trial for TTV-guided immunosuppression in adult kidney recipients (TTVguideIT) began in 2022. There is, therefore, great promise for TTV levels to be used as a biomarker that could potentially improve both graft and patient survival in transplantation., (© 2024 The Author(s). Pediatric Transplantation published by Wiley Periodicals LLC.)

Published
2024
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35. Epidemiological and Clinical Insights into the Enterovirus D68 Upsurge in Europe 2021-2022 and Emergence of Novel B3-Derived Lineages, ENPEN Multicentre Study.

Author

Simoes MP, Hodcroft EB, Simmonds P, Albert J, Alidjinou EK, Ambert-Balay K, Andrés C, Antón A, Auvray C, Bailly JL, Baldanti F, Bastings C, Beard S, Berengua C, Berginc N, Bloemen M, Blomqvist S, Bosma F, Böttcher S, Bubba L, Buderus S, Cabrerizo M, Calvo C, Celma C, Ceriotti F, Clark G, Costa I, Coste-Burel M, Couderé K, Cremer J, Del Cuerpo Casas M, Daehne T, de Beer J, de Ceano-Vivas M, De Gascun C, de Rougemont A, Dean J, Dembinski JL, Diedrich S, Diez-Domingo J, Dillner L, Dorenberg DH, Ducancelle A, Dudman S, Dyrdak R, Eis-Huebinger AM, Falces-Romero I, Farkas A, Feeney S, Fernandez-Garcia MD, Flipse J, Franck KT, Galli C, Garrigue I, Geeraedts F, Georgieva I, Giardina F, Guiomar R, Hauzenberger E, Heikens E, Henquell C, Hober D, Hönemann M, Howson-Wells H, Hruškar Ž, Ikonen N, Imbert B, Jansz AR, Jeannoël M, Jiřincová H, Josset L, Keeren K, Kramer-Lindhout N, Krokstad S, Lazrek M, Le Guillou-Guillemette H, Lefeuvre C, Lind A, Lunar MM, Maier M, Marque-Juillet S, McClure CP, McKenna J, Meijer A, Menasalvas Ruiz A, Mengual-Chuliá B, Midgley S, Mirand A, Molenkamp R, Montes M, Moreno-Docón A, Morley U, Murk JL, Navascués-Ortega A, Nijhuis R, Nikolaeva-Glomb L, Nordbø SA, Numanovic S, Oggioni M, Oñate Vergara E, Pacaud J, Pacreau ML, Panning M, Pariani E, Pekova L, Pellegrinelli L, Petrovec M, Pietsch C, Pilorge L, Piñeiro L, Piralla A, Poljak M, Prochazka B, Rabella N, Rahamat-Langendoen JC, Rainetova P, Reynders M, Riezebos-Brilman A, Roorda L, Savolainen-Kopra C, Schuffenecker I, Smeets LC, Stoyanova A, Stefic K, Swanink C, Tabain I, Tjhie J, Thouault L, Tumiotto C, Uceda Renteria S, Uršič T, Vallet S, Van Ranst M, Van Wunnik P, Verweij JJ, Vila J, Wintermans B, Wollants E, Wolthers KC, Xavier López-Labrador F, Fischer TK, Harvala H, and Benschop KSM

Subjects
Humans, Europe epidemiology, Child, Preschool, Male, Infant, Female, Child, Adolescent, Myelitis epidemiology, Myelitis virology, Respiratory Tract Infections virology, Respiratory Tract Infections epidemiology, Adult, Central Nervous System Viral Diseases epidemiology, Central Nervous System Viral Diseases virology, Infant, Newborn, Young Adult, Middle Aged, Neuromuscular Diseases epidemiology, Neuromuscular Diseases virology, Aged, Enterovirus Infections epidemiology, Enterovirus Infections virology, Enterovirus D, Human genetics, Enterovirus D, Human classification, Enterovirus D, Human isolation & purification, Phylogeny
Abstract

Enterovirus D68 (EV-D68) infections are associated with severe respiratory disease and acute flaccid myelitis (AFM). The European Non-Polio Enterovirus Network (ENPEN) aimed to investigate the epidemiological and genetic characteristics of EV-D68 infections and its clinical impact during the fall-winter season of 2021-2022. From 19 European countries, 58 institutes reported 10 481 (6.8%) EV-positive samples of which 1004 (9.6%) were identified as EV-D68 (including 852 respiratory samples). Clinical data were reported for 969 cases; 78.9% of infections were reported in children (0-5 years); and 37.9% of cases were hospitalized. Acute respiratory distress was commonly noted (93.1%) followed by fever (49.4%). Neurological problems were observed in 6.4% of cases including 6 diagnosed with AFM. Phylodynamic/Nextstrain and phylogenetic analyses based on 694 sequences showed the emergence of 2 novel B3-derived lineages, with no regional clustering. In conclusion, we describe a large-scale European EV-D68 upsurge with severe clinical impact and the emergence of B3-derived lineages., Competing Interests: Potential conflicts of interest. All authors: No reported conflicts of interest. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed., (© The Author(s) 2024. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)

Published
2024
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36. Detection of hepatitis E RNA in pork products at point of retail in Ireland - Are consumers at risk?

Author

Bennett C, Coughlan S, Hunt K, Butler F, Fanning S, Ryan E, De Gascun C, and O'Gorman J

Subjects
Humans, Animals, Swine, Ireland epidemiology, Sus scrofa, RNA, Viral genetics, RNA, Viral analysis, Hepatitis E epidemiology, Hepatitis E virus genetics, Meat Products analysis, Pork Meat analysis, Red Meat, Swine Diseases epidemiology
Abstract

Hepatitis E (HEV), a zoonotic virus, is the leading cause of acute viral hepatitis in Europe. The presence of HEV in domestic pigs can result in infections in humans through consumption of pork products which are undercooked or where processing methods are insufficient to inactivate the virus. In Ireland, pork accounts for 34 % of all meat consumption (CSO, 2022) and the prevalence of HEV in products at point of retail has not previously been characterised. A sampling strategy was designed in which high pork content sausages, fresh pork liver and raw fermented sausages were systematically purchased from three types of retailers between May 2018 and March 2019. In total, 200 pork products were tested using a lysing agent to release the HEV from the product for detection. RT-PCR for HEV was performed on samples with an extraction efficiency >1 % (n = 188/200) (94 %). Low level HEV RNA was detected in 9/188 (4.8 %) pork products tested. The highest incidence of HEV RNA was in pork liver where 6/25 (24 %) samples were positive. The concentration of HEV ranged from 0.02 - to 9.4 genome copies/g of pork. Based on these data an exposure assessment was performed which found that if consumers followed advice from the Food Safety Authority of Ireland to achieve core temperatures of 70 °C or higher when cooking, the risk was likely to be negligible., Competing Interests: Declaration of competing interest None., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Published
2024
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37. Whole-genome sequencing to investigate transmission of SARS-CoV-2 in the acute healthcare setting: a systematic review.

Author

Hare D, Dembicka KM, Brennan C, Campbell C, Sutton-Fitzpatrick U, Stapleton PJ, De Gascun CF, and Dunne CP

Subjects
Humans, SARS-CoV-2 genetics, Disease Outbreaks prevention & control, Delivery of Health Care, COVID-19 epidemiology, COVID-19 prevention & control, Cross Infection epidemiology, Cross Infection prevention & control
Abstract

Background: Whole-genome sequencing (WGS) has been used widely to elucidate transmission of SARS-CoV-2 in acute healthcare settings, and to guide infection, prevention, and control (IPC) responses., Aim: To systematically appraise available literature, published between January 1 st , 2020 and June 30 th , 2022, describing the implementation of WGS in acute healthcare settings to characterize nosocomial SARS-CoV-2 transmission., Methods: Searches of the PubMed, Embase, Ovid MEDLINE, EBSCO MEDLINE, and Cochrane Library databases identified studies in English reporting the use of WGS to investigate SARS-CoV-2 transmission in acute healthcare environments. Publications involved data collected up to December 31 st , 2021, and findings were reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement., Findings: In all, 3088 non-duplicate records were retrieved; 97 met inclusion criteria, involving 62 outbreak analyses and 35 genomic surveillance studies. No publications from low-income countries were identified. In 87/97 (90%), WGS supported hypotheses for nosocomial transmission, while in 46 out of 97 (47%) suspected transmission events were excluded. An IPC intervention was attributed to the use of WGS in 18 out of 97 (18%); however, only three (3%) studies reported turnaround times ≤7 days facilitating near real-time IPC action, and none reported an impact on the incidence of nosocomial COVID-19 attributable to WGS., Conclusion: WGS can elucidate transmission of SARS-CoV-2 in acute healthcare settings to enhance epidemiological investigations. However, evidence was not identified to support sequencing as an intervention to reduce the incidence of SARS-CoV-2 in hospital or to alter the trajectory of active outbreaks., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Published
2023
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38. Detection of Hepatitis A RNA, Hepatitis E RNA, Human Adenovirus F DNA, and Norovirus RNA in Fresh and Frozen Berry Products at Point of Retail in Ireland.

Author

Bennett C, Hunt K, Butler F, Keaveney S, Fanning S, De Gascun C, Coughlan S, and O'Gorman J

Subjects
Humans, Fruit, Food Microbiology, Ireland, RNA, Viral genetics, RNA, Viral analysis, DNA, Food Contamination analysis, Adenoviruses, Human genetics, Hepatitis A, Hepatitis E, Norovirus genetics, Hepatitis A virus genetics, Nucleic Acids
Abstract

Soft fruits are at particular risk of contamination with enteric viruses such as Hepatitis A virus (HAV), Hepatitis E Virus (HEV), Norovirus (NoV), Human Adenovirus (HAdV) and Sapovirus (SaV). The aim of this study was to investigate, for the first time, the presence of these biological agents in ready to eat (RTE) berries at point of retail in Ireland. A sampling strategy was designed in which RTE fresh and frozen strawberries and raspberries were purchased from five retailers between May and October 2018. Reverse Transcriptase Polymerase Chain Reaction (RT-qPCR) assays for HEV RNA, Nov RNA, SaV RNA, and human Adenovirus species F DNA (HAdV-F) were performed on 239 samples (25g portions). Viral nucleic acid was present in 6.7% (n = 16) of samples tested as follows: HAV RNA (n = 5), HAdV-F DNA (n = 5), HEV RNA (n = 3) and NoV GII RNA (n = 3). Sapovirus RNA was not detected in any product. No significant differences were found between berry type, fresh/frozen status, or supermarket source. This study suggests a risk that exists across all retail outlets however only low levels of nucleic acid ranging from 0 to 16 genome copies/g were present. Although these findings may reflect non-viable/non-infectious virus the continued provision of risk mitigation advice to consumers is warranted and further work is required to ensure control measures to reduce contamination are implemented and enforced., (© 2023. The Author(s).)

Published
2023
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39. New perspectives on respiratory syncytial virus surveillance at the national level: lessons from the COVID-19 pandemic.

Author

Teirlinck AC, Johannesen CK, Broberg EK, Penttinen P, Campbell H, Nair H, Reeves RM, Bøås H, Brytting M, Cai W, Carnahan A, Casalegno JS, Danis K, De Gascun C, Ellis J, Emborg HD, Gijon M, Guiomar R, Hirve SS, Jiřincová H, Nohynek H, Oliva JA, Osei-Yeboah R, Paget J, Pakarna G, Pebody R, Presser L, Rapp M, Reiche J, Rodrigues AP, Seppälä E, Socan M, Szymanski K, Trebbien R, Večeřová J, van der Werf S, Zambon M, Meijer A, and Fischer TK

Subjects
Humans, Pandemics, COVID-19 epidemiology, Respiratory Syncytial Virus, Human, Respiratory Syncytial Virus Infections epidemiology, Respiratory Tract Infections epidemiology
Abstract

Competing Interests: Conflict of interest: The content of the workshop on RSV surveillance was organised by SSI, RIVM and ECDC. This workshop was organised as an element of the Respiratory Syncytial Virus Consortium in Europe (RESCEU). RESCEU has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement 116019. This Joint Undertaking receives support from the EU's Horizon 2020 research and innovation programme and the European Federation of Pharmaceutical Industries and Associations. This workshop was only attended by publicly funded participants of academic and public health bodies. No industrial partners participated in the meeting or were involved in writing this manuscript. The institutions of the following co-authors are partners in RESCEU: National Institute for Public Health and the Environment, RIVM, the Netherlands (A.C. Teirlinck, A. Meijer, L. Presser); Statens Serum Institute, SSI, Denmark (T.K. Fischer, R. Trebbien, H-D. Emborg and C.K. Johannesen); University of Edinburgh (H. Nair, H. Campbell, R. Osei-Yeboah); PENTA (M. Gijjon). The institutions of the following co-authors are affiliated partners in RESCEU: Norwegian Institute of Public Health (H. Bøås, E. Seppälä); Nivel, the Netherlands (J. Paget), Finnish Institute for Health and Welfare THL (H. Nohynek). E.K. Broberg and P. Penttinen (both ECDC) are members of the Scientific Advisory Group of RESCEU. H. Nohynek reports grants from GSK, Sanofi-Pasteur and Pfizer (to their institute THL, not their unit), outside the submitted work; and membership of the ESWI Scientific Committee. In addition, H. Nohynek has participated on data safety monitoring boards related to COVID-19 and Pertussis vaccines. J. Paget reports unrestricted research grants from Sanofi Pasteur, WHO, and Foundation for Influenza Epidemiology to Nivel, outside the submitted work. A.P. Rodrigues reports grants from AstraZeneca and Sanofi-Pasteur, and travel support from AstraZeneca, outside the submitted work. H. Nair reports grants from IMI, NIHR, WHO and Pfizer, consulting fees from BMGF, honoraria from AstraZeneca (all to their institute) and participated in DSM boards/advisory boards for Sanofi, ReViral, Novavax and GSK outside the submitted work. H. Campbell reports grants from EU IMI to the University of Edinburgh during the conduct of the study. H. Campbell also reports grants, consulting fees and travel support from WHO, BMGF and Sanofi (all paid via the University of Edinburgh). R.M. Reeves reports employment by IQVIA Real-World Solutions, and honoraria for manuscript writing from Sanofi Pasteur, both outside the submitted work. S. van der Werf reports a grant from Sanofi Pasteur, patents and participation in data safety monitoring boards and advisory boards, all outside the submitted work. C. De Gascun reports lecture honoraria from Sanofi-Aventis Ireland Limited, outside the submitted work. All other authors report no conflicts of interest outside the submitted work.

Published
2023
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40. A viral metagenomic protocol for nanopore sequencing of group A rotavirus.

Author

Yandle Z, Gonzalez G, Carr M, Matthijnssens J, and De Gascun C

Subjects
Humans, Phylogeny, Polymerase Chain Reaction, Genome, Viral, Genotype, Rotavirus genetics, Nanopore Sequencing, Rotavirus Infections
Abstract

Aim: Development of an unbiased methodology using Oxford Nanopore Technology (ONT) sequencing to obtain whole-genome sequences (WGS) of Rotavirus A (RVA) from clinical samples., Methods: 157 RVA qRT-PCR positive faecal samples were enriched by virus-like particle (VLP) purification and host nuclease digestion to enhance the detection of viral nucleic acids and cDNA generated as per the NetoVIR protocol. ONT sequencing was then performed using the ONT Native Barcoding kit (SQK-LSK-109) on the GridION platform. Data was basecalled, demultiplexed and assembled into near complete RVA genomes. The accuracy and quality of the obtained sequences was assessed by comparing to Sanger sequencing and RVA reference genomes., Results: The developed protocol generated 146 near-complete RVA WGS out of the 157 RVA-positive clinical samples. The quality of the assembled genomes was assessed by comparison against publicly-available sequences with results showing 98.76 % ± 0.03 % similarity and > 90 % genome coverage. A concordance assessment was performed comparing the identity of partial RVA VP7 and VP4 segments obtained by Sanger sequencing (n = 51) against corresponding nanopore sequences which demonstrated an overall identity of 100.0 % ± 0.02 %., Conclusions: The nanopore protocol generated both high quality and accurate RVA WGS extracted from faecal samples. This protocol can be extended to other viral agents in other sample types., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Published
2023
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41. Mumps-specific IgG, IgG subclasses and neutralization titres to the vaccine and outbreak mumps strains differ in vaccinated healthy controls, breakthrough mumps infection cases and naturally infected individuals.

Author

Foley DJ, Connell AR, Gonzalez G, Connell J, Leahy TR, De Gascun C, and Hassan J

Subjects
Humans, Mumps virus genetics, Mumps Vaccine, Antibodies, Viral, Neutralization Tests, Immunoglobulin G, Disease Outbreaks, Mumps epidemiology, Mumps prevention & control
Abstract

Background: Despite widespread use of the mumps vaccine resulting in significant reduction in the incidence of symptomatic mumps infection, large outbreaks continue to occur in highly vaccinated populations., Objectives: We examined the mumps-specific IgG, IgG subclasses and neutralization titres to the outbreak Genotype G5 and Jeryl Lynn vaccine (Genotype A) mumps strains., Study Design: Sera from 207 individuals were classified into five distinct cohorts: healthy controls and mumps cases of 5-17 years and 18-25 years, and naturally infected individuals of 50+ years. Mumps specific IgG and IgG subclass levels were measured using modified ELISA assays with lysates and nucleoprotein antigens from both the mumps vaccine and circulating Genotype G5 strains. All sera were investigated for in vitro neutralizing antibody titres (GMT) using focus reduction neutralization assays. Data was analysed using the Kruskal-Wallis test and pairwise Wilcoxon tests., Results: Mumps cases had higher mumps IgG levels compared to controls, to both the vaccine and outbreak strains, however levels decreased with age. Mumps IgG3 levels were significantly raised in mumps cases (p < 0.001). Neutralization titres were lower to the outbreak strain in all cohorts with titres markedly lower in the mumps cohorts compared to healthy controls. Mean GMT to the vaccine strain increased with age. The naturally infected group displayed the highest GMT to the JL vaccine and the lowest GMT to the outbreak strain., Conclusions: Antigenic differences between mumps vaccine strain and circulating mumps viruses decrease the cross-neutralization capacity of vaccine-induced antibodies which may play a role in breakthrough infection., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022. Published by Elsevier B.V.)

Published
2022
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42. SARS-CoV-2 variant trends in Ireland: Wastewater-based epidemiology and clinical surveillance.

Author

Reynolds LJ, Gonzalez G, Sala-Comorera L, Martin NA, Byrne A, Fennema S, Holohan N, Kuntamukkula SR, Sarwar N, Nolan TM, Stephens JH, Whitty M, Bennett C, Luu Q, Morley U, Yandle Z, Dean J, Joyce E, O'Sullivan JJ, Cuddihy JM, McIntyre AM, Robinson EP, Dahly D, Fletcher NF, Carr M, De Gascun C, and Meijer WG

Subjects
Humans, Ireland epidemiology, RNA, Viral, Wastewater analysis, Wastewater-Based Epidemiological Monitoring, COVID-19 epidemiology, SARS-CoV-2 genetics
Abstract

SARS-CoV-2 RNA quantification in wastewater is an important tool for monitoring the prevalence of COVID-19 disease on a community scale which complements case-based surveillance systems. As novel variants of concern (VOCs) emerge there is also a need to identify the primary circulating variants in a community, accomplished to date by sequencing clinical samples. Quantifying variants in wastewater offers a cost-effective means to augment these sequencing efforts. In this study, SARS-CoV-2 N1 RNA concentrations and daily loadings were determined and compared to case-based data collected as part of a national surveillance programme to determine the validity of wastewater surveillance to monitor infection spread in the greater Dublin area. Further, sequencing of clinical samples was conducted to determine the primary SARS-CoV-2 lineages circulating in Dublin. Finally, digital PCR was employed to determine whether SARS-CoV-2 VOCs, Alpha and Delta, were quantifiable from wastewater. No lead or lag time was observed between SARS-CoV-2 wastewater and case-based data and SARS-CoV-2 trends in Dublin wastewater significantly correlated with the notification of confirmed cases through case-based surveillance preceding collection with a 5-day average. This demonstrates that viral RNA in Dublin's wastewater mirrors the spread of infection in the community. Clinical sequence data demonstrated that increased COVID-19 cases during Ireland's third wave coincided with the introduction of the Alpha variant, while the fourth wave coincided with increased prevalence of the Delta variant. Interestingly, the Alpha variant was detected in Dublin wastewater prior to the first genome being sequenced from clinical samples, while the Delta variant was identified at the same time in clinical and wastewater samples. This work demonstrates the validity of wastewater surveillance for monitoring SARS-CoV-2 infections and also highlights its effectiveness in identifying circulating variants which may prove useful when sequencing capacity is limited., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

Published
2022
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43. Repeated transmission of SARS-CoV-2 in an overcrowded Irish emergency department elucidated by whole-genome sequencing.

Author

Hare D, Meaney C, Powell J, Slevin B, O' Brien B, Power L, O' Connell NH, De Gascun CF, Dunne CP, and Stapleton PJ

Subjects
Genome, Viral, Humans, Ireland epidemiology, Pandemics prevention & control, Phylogeny, SARS-CoV-2 genetics, Whole Genome Sequencing, COVID-19 epidemiology, COVID-19 transmission, Cross Infection epidemiology, Cross Infection virology, Emergency Service, Hospital
Abstract

Aim: To provide a detailed genomic-epidemiological description of a complex multi-ward SARS-CoV-2 outbreak, which originated in the crowded emergency department (ED) in our hospital during the third wave of the COVID-19 pandemic, and was elucidated promptly by local whole-genome sequencing (WGS)., Methods: SARS-CoV-2 was detected by reverse transcriptase real-time polymerase chain reaction on viral RNA extracted from nasopharyngeal swabs. WGS was performed using an Oxford MinION Mk1C instrument following the ARTIC v3 sequencing protocol. High-quality consensus genomes were assembled with the artic-ncov2019 bioinformatics pipeline and viral phylogenetic trees were built, inferred by maximum-likelihood. Clusters were defined using a threshold of 0-1 single nucleotide polymorphisms (SNPs) between epidemiologically linked sequences., Results: In April 2021, outbreaks of COVID-19 were declared on two wards at University Hospital Limerick after 4 healthcare-associated SARS-CoV-2 infections were detected by post-admission surveillance testing. Contact tracing identified 12 further connected cases; all with direct or indirect links to the ED 'COVID Zone'. All sequences were assigned to the Pangolin B.1.1.7 lineage by WGS, and SNP-level analysis revealed two distinct but simultaneous clusters of infections. Repeated transmission in the ED was demonstrated, involving patients accommodated on trolleys in crowded areas, resulting in multiple generations of infections across three inpatient hospital wards and subsequently to the local community. These findings informed mitigation efforts to prevent cross-transmission in the ED., Conclusion: Cross-transmission of SARS-CoV-2 occurred repeatedly in an overcrowded emergency department. Viral WGS elucidated complex viral transmission networks in our hospital and informed infection, prevention and control practice., (Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Published
2022
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45. Quantifying the risk of SARS-CoV-2 reinfection over time.

Author

O Murchu E, Byrne P, Carty PG, De Gascun C, Keogan M, O'Neill M, Harrington P, and Ryan M

Subjects
Aged, COVID-19 Vaccines, Humans, Pandemics, COVID-19 diagnosis, COVID-19 epidemiology, Reinfection, SARS-CoV-2
Abstract

Despite over 140 million SARS-CoV-2 infections worldwide since the beginning of the pandemic, relatively few confirmed cases of SARS-CoV-2 reinfection have been reported. While immunity from SARS-CoV-2 infection is probable, at least in the short term, few studies have quantified the reinfection risk. To our knowledge, this is the first systematic review to synthesise the evidence on the risk of SARS-CoV-2 reinfection over time. A standardised protocol was employed, based on Cochrane methodology. Electronic databases and preprint servers were searched from 1 January 2020 to 19 February 2021. Eleven large cohort studies were identified that estimated the risk of SARS-CoV-2 reinfection over time, including three that enrolled healthcare workers and two that enrolled residents and staff of elderly care homes. Across studies, the total number of PCR-positive or antibody-positive participants at baseline was 615,777, and the maximum duration of follow-up was more than 10 months in three studies. Reinfection was an uncommon event (absolute rate 0%-1.1%), with no study reporting an increase in the risk of reinfection over time. Only one study estimated the population-level risk of reinfection based on whole genome sequencing in a subset of patients; the estimated risk was low (0.1% [95% CI: 0.08-0.11%]) with no evidence of waning immunity for up to 7 months following primary infection. These data suggest that naturally acquired SARS-CoV-2 immunity does not wane for at least 10 months post-infection. However, the applicability of these studies to new variants or to vaccine-induced immunity remains uncertain., (© 2021 John Wiley & Sons Ltd.)

Published
2022
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46. Routine screening for hepatitis C in pregnancy is cost-effective in a large urban population in Ireland: a retrospective study.

Author

McCormick CA, Domegan L, Carty PG, Drew R, McAuliffe FM, O'Donohoe O, White N, Garvey P, O'Grady M, De Gascun CF, and McCormick PA

Subjects
Cost-Benefit Analysis, Female, Hepatitis C blood, Hepatitis C diagnosis, Humans, Ireland, Pregnancy, Pregnancy Complications, Infectious blood, Pregnancy Complications, Infectious diagnosis, Retrospective Studies, Risk Factors, Urban Population, Hepacivirus isolation & purification, Hepatitis C prevention & control, Pregnancy Complications, Infectious prevention & control, Prenatal Diagnosis economics
Abstract

Objective: To investigate whether risk factor-based screening in pregnancy is failing to identify women with hepatitis C virus (HCV) infection and to assess the cost-effectiveness of universal screening., Design: Retrospective study and model-based economic evaluation., Setting: Two urban tertiary referral maternity units, currently using risk factor-based screening for HCV infection., Population: Pregnant women who had been tested for hepatitis B, HIV but not HCV., Methods: Anonymised sera were tested for HCV antibody. Positive sera were tested for HCV antigen. A cost-effectiveness analysis of a change to universal screening was performed using a Markov model to simulate disease progression and Monte Carlo simulations for probabilistic sensitivity analysis., Main Outcome Measures: Presence of HCV antigen and cost per quality-adjusted life year (QALY)., Results: In all, 4655 samples were analysed. Twenty had HCV antibodies and five HCV antigen. This gives an active infection rate of 5/4655, or 0.11%, compared with a rate of 0.15% in the risk-factor group. This prevalence is 65% lower than a previous study in the same hospitals from 2001 to 2005. The calculated incremental cost-effectiveness ratio (ICER) for universal screening was €3,315 per QALY gained., Conclusion: This study showed that the prevalence of HCV infection in pregnant women in the Dublin region has declined by 65% over the past two decades. Risk factor-based screening misses a significant proportion of infections. A change to universal maternal screening for hepatitis C would be cost-effective in our population., Tweetable Abstract: Universal maternal screening for hepatitis C is cost-effective in this urban Irish population., (© 2021 John Wiley & Sons Ltd.)

Published
2022
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47. Re-emergence of enterovirus D68 in Europe after easing the COVID-19 lockdown, September 2021.

Author

Benschop KS, Albert J, Anton A, Andrés C, Aranzamendi M, Armannsdóttir B, Bailly JL, Baldanti F, Baldvinsdóttir GE, Beard S, Berginc N, Böttcher S, Blomqvist S, Bubba L, Calvo C, Cabrerizo M, Cavallero A, Celma C, Ceriotti F, Costa I, Cottrell S, Del Cuerpo M, Dean J, Dembinski JL, Diedrich S, Diez-Domingo J, Dorenberg D, Duizer E, Dyrdak R, Fanti D, Farkas A, Feeney S, Flipse J, De Gascun C, Galli C, Georgieva I, Gifford L, Guiomar R, Hönemann M, Ikonen N, Jeannoël M, Josset L, Keeren K, López-Labrador FX, Maier M, McKenna J, Meijer A, Mengual-Chuliá B, Midgley SE, Mirand A, Montes M, Moore C, Morley U, Murk JL, Nikolaeva-Glomb L, Numanovic S, Oggioni M, Palminha P, Pariani E, Pellegrinelli L, Piralla A, Pietsch C, Piñeiro L, Rabella N, Rainetova P, Uceda Renteria SC, Romero MP, Reynders M, Roorda L, Savolainen-Kopra C, Schuffenecker I, Soynova A, Swanink CM, Ursic T, Verweij JJ, Vila J, Vuorinen T, Simmonds P, Fischer TK, and Harvala H

Subjects
Communicable Disease Control, Disease Outbreaks, Europe epidemiology, Humans, SARS-CoV-2, COVID-19, Enterovirus, Enterovirus D, Human genetics, Enterovirus Infections diagnosis, Enterovirus Infections epidemiology, Myelitis epidemiology, Respiratory Tract Infections
Abstract

We report a rapid increase in enterovirus D68 (EV-D68) infections, with 139 cases reported from eight European countries between 31 July and 14 October 2021. This upsurge is in line with the seasonality of EV-D68 and was presumably stimulated by the widespread reopening after COVID-19 lockdown. Most cases were identified in September, but more are to be expected in the coming months. Reinforcement of clinical awareness, diagnostic capacities and surveillance of EV-D68 is urgently needed in Europe.

Published
2021
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48. Review Article: vaccination for patients with inflammatory bowel disease during the COVID-19 pandemic.

Author

Doherty J, Fennessy S, Stack R, O' Morain N, Cullen G, Ryan EJ, De Gascun C, and Doherty GA

Subjects
COVID-19 Vaccines, Humans, Pandemics, SARS-CoV-2, Tumor Necrosis Factor Inhibitors, Vaccination, COVID-19, Inflammatory Bowel Diseases
Abstract

Background: Poor immune responses are frequently observed in patients with inflammatory bowel disease (IBD) receiving established vaccines; risk factors include immunosuppressants and active disease., Aims: To summarise available information regarding immune responses achieved in patients with IBD receiving established vaccines. Using this information, to identify risk factors in the IBD population related to poor vaccine-induced immunity that may be applicable to vaccines against COVID-19., Methods: We undertook a literature review on immunity to currently recommended vaccines for patients with IBD and to COVID-19 vaccines and summarised the relevant literature., Results: Patients with IBD have reduced immune responses following vaccination compared to the general population. Factors including the use of immunomodulators and anti-TNF agents reduce response rates. Patients with IBD should be vaccinated against COVID-19 at the earliest opportunity as recommended by International Advisory Committees, and vaccination should not be deferred because a patient is receiving immune-modifying therapies. Antibody titres to COVID-19 vaccines appear to be reduced in patients receiving anti-TNF therapy, especially in combination with immunomodulators after one vaccination. Therefore, we should optimise any established risk factors that could impact response to vaccination in patients with IBD before vaccination., Conclusions: Ideally, patients with IBD should be vaccinated at the earliest opportunity against COVID-19. Patients should be in remission and, if possible, have their corticosteroid dose minimised before vaccination. Further research is required to determine the impact of different biologics on vaccine response to COVID-19 and the potential for booster vaccines or heterologous prime-boost vaccinations in the IBD population., (© 2021 The Authors. Alimentary Pharmacology & Therapeutics published by John Wiley & Sons Ltd.)

Published
2021
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49. SARS-CoV-2 Antibody Testing in Health Care Workers: A Comparison of the Clinical Performance of Three Commercially Available Antibody Assays.

Author

Allen N, Brady M, Carrion Martin AI, Domegan L, Walsh C, Houlihan E, Kerr C, Doherty L, King J, Doheny M, Griffin D, Molloy M, Dunne J, Crowley V, Holmes P, Keogh E, Naughton S, Kelly M, O'Rourke F, Lynagh Y, Crowley B, de Gascun C, Holder P, Bergin C, Fleming C, Ni Riain U, and Conlon N

Subjects
Adult, Cross-Sectional Studies, Enzyme-Linked Immunosorbent Assay, Female, Health Personnel statistics & numerical data, Humans, Immunoglobulin G blood, Male, Middle Aged, Phosphoproteins immunology, Sensitivity and Specificity, Seroepidemiologic Studies, Young Adult, Antibodies, Viral blood, COVID-19 diagnosis, COVID-19 Serological Testing methods, Coronavirus Nucleocapsid Proteins immunology, SARS-CoV-2 immunology, Spike Glycoprotein, Coronavirus immunology
Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies are an excellent indicator of past COVID-19 infection. As the COVID-19 pandemic progresses, retained sensitivity over time is an important quality in an antibody assay that is to be used for the purpose of population seroprevalence studies. We compared 5,788 health care worker (HCW) serum samples by using two serological assays (Abbott SARS-CoV-2 anti-nucleocapsid immunoglobulin G (IgG) and Roche anti-SARS-CoV-2 anti-nucleocapsid total antibody) and a subset of samples (all Abbott assay positive or grayzone, n  = 485) on Wantai SARS-CoV-2 anti-spike antibody enzyme-linked immunosorbent assay (ELISA). For 367 samples from HCW with a previous PCR-confirmed SARS-CoV-2 infection, we correlated the timing of infection with assay results. Overall, seroprevalence was 4.2% on Abbott and 9.5% on Roche. Of those with previously confirmed infection, 41% (150/367) and 95% (348/367) tested positive on Abbott and Roche, respectively. At 21 weeks (150 days) after confirmed infection, positivity on Abbott started to decline. Roche positivity was retained for the entire study period (33 weeks). Factors associated ( P ≤ 0.050) with Abbott seronegativity in those with previous PCR-confirmed infection included sex (odds ratio [OR], 0.30 male ; 95% confidence interval [CI], 0.15 to 0.60), symptom severity (OR 0.19 severe symptoms; 95% CI, 0.05 to 0.61), ethnicity (OR, 0.28 Asian ethnicity; 95% CI, 0.12 to 0.60), and time since PCR diagnosis (OR, 2.06 for infection 6 months previously; 95% CI, 1.01 to 4.30). Wantai detected all previously confirmed infections. In our population, Roche detected antibodies up to at least 7 months after natural infection with SARS-CoV-2. This finding indicates that the Roche total antibody assay is better suited than Abbott IgG assay to population-based studies. Wantai demonstrated high sensitivity, but sample selection was biased. The relationship between serological response and functional immunity to SARS-CoV-2 infection needs to be delineated. IMPORTANCE As the COVID-19 pandemic progresses, retained sensitivity over time is an important quality in an antibody assay that is to be used for the purpose of population seroprevalence studies. There is a relative paucity of published literature in this field to help guide public health specialists when planning seroprevalence studies. In this study, we compared results of 5,788 health care worker blood samples tested by using two assays (Roche and Elecsys, anti-nucleocapsid antibody) and by testing a subset on a third assay (Wantai enzyme-linked immunosorbent assay [ELISA] anti-spike antibody). We found significant differences in the performance of these assays, especially with distance in time from PCR-confirmed COVID-19 infection, and we feel these results may significantly impact the choice of assay for others conducting similar studies.

Published
2021
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50. Immunological assessment of SARS-CoV-2 infection in pregnancy from diagnosis to delivery: A multicentre prospective study.

Author

Glennon K, Donnelly J, Knowles S, McAuliffe FM, O'Reilly A, Corcoran S, Walsh J, McMorrow R, Higgins T, Bolger L, Clinton S, O'Riordan S, Start A, Roche D, Bartels H, Malone C, McAuley K, McDermott A, Inzitari R, O'Donnell CPF, Malone F, Higgins S, De Gascun C, Doran P, and Brennan DJ

Subjects
Antibody Formation immunology, COVID-19 genetics, COVID-19 virology, Female, Fetal Blood metabolism, Follow-Up Studies, Humans, Immunoglobulin G immunology, Immunoglobulin M immunology, Longitudinal Studies, Pregnancy, Prospective Studies, COVID-19 diagnosis, COVID-19 immunology, Delivery, Obstetric, SARS-CoV-2 immunology
Abstract

Background: Background Population-based data on SARS-CoV-2 infection in pregnancy and assessment of passive immunity to the neonate, is lacking. We profiled the maternal and fetal response using a combination of viral RNA from naso-pharyngeal swabs and serological assessment of antibodies against SARS-CoV-2., Methods: This multicentre prospective observational study was conducted between March 24th and August 31st 2020. Two independent cohorts were established, a symptomatic SARS-CoV-2 cohort and a cohort of asymptomatic pregnant women attending two of the largest maternity hospitals in Europe. Symptomatic women were invited to provide a serum sample to assess antibody responses. Asymptomatic pregnant women provided a nasopharyngeal swab and serum sample. RT-PCR for viral RNA was performed using the Cobas SARS-CoV-2 6800 platform (Roche). Umbilical cord bloods were obtained at delivery. Maternal and fetal serological response was measured using both the Elecsys® Anti-SARS-CoV-2 immunoassay (Roche), Abbott SARS-CoV-2 IgG Assay and the IgM Architect assay. Informed written consent was obtained from all participants., Results: Ten of twenty three symptomatic women had SARS-CoV-2 RNA detected on nasopharyngeal swabs. Five (5/23, 21.7%) demonstrated serological evidence of anti-SARS-CoV-2 IgG antibodies and seven (30.4%, 7/23) were positive for IgM antibodies. In the asymptomatic cohort, the prevalence of SARS-CoV-2 infection in RNA was 0.16% (1/608). IgG SARS-CoV-2 antibodies were detected in 1·67% (10/598, 95% CI 0·8%-3·1%) and IgM in 3·51% (21/598, 95% CI 2·3-5·5%). Nine women had repeat testing post the baseline test. Four (4/9, 44%) remained IgM positive and one remained IgG positive. 3 IgG anti-SARS-CoV-2 antibodies were detectable in cord bloods from babies born to five seropositive women who delivered during the study. The mean gestation at serological test was 34 weeks. The mean time between maternal serologic positivity and detection in umbilical cord samples was 28 days., Conclusion: Using two independent serological assays, we present a comprehensive illustration of the antibody response to SARS-CoV-2 in pregnancy, and show a low prevalence of asymptomatic SARS-CoV2. Transplacental migration of anti-SARS-CoV-2 antibodies was identified in cord blood of women who demonstrated antenatal anti-SARS-CoV-2 antibodies, raising the possibility of passive immunity., Competing Interests: The authors have declared that no competing interests exist.

Published
2021
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