47 results on '"Vihta, Karina-Doris"'
Search Results
2. SARS-CoV-2, influenza A/B and respiratory syncytial virus positivity and association with influenza-like illness and self-reported symptoms, over the 2022/23 winter season in the UK: a longitudinal surveillance cohort
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Dietz, Elisabeth, Pritchard, Emma, Pouwels, Koen, Ehsaan, Muhammad, Blake, Joshua, Gaughan, Charlotte, Haduli, Eric, Boothe, Hugh, Vihta, Karina-Doris, Peto, Tim, Stoesser, Nicole, Matthews, Philippa, Taylor, Nick, Diamond, Ian, Studley, Ruth, Rourke, Emma, Birrell, Paul, De Angelis, Daniela, Fowler, Tom, Watson, Conall, Eyre, David, House, Thomas, and Walker, Ann Sarah
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- 2024
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3. The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies
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Lipworth, Samuel, Matlock, William, Shaw, Liam, Vihta, Karina-Doris, Rodger, Gillian, Chau, Kevin, Barker, Leanne, George, Sophie, Kavanagh, James, Davies, Timothy, Vaughan, Alison, Andersson, Monique, Jeffery, Katie, Oakley, Sarah, Morgan, Marcus, Hopkins, Susan, Peto, Timothy, Crook, Derrick, Walker, A. Sarah, and Stoesser, Nicole
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- 2024
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4. Cycle Threshold Values as Indication of Increasing SARS-CoV-2 New Variants, England, 2020-2022
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Harrison, Rebecca E., Hamada, Ahmed, Haswell, Nujcharee, Groves, Aigul, Vihta, Karina-Doris, Cella, Kerry, Garner, Sarah, Walker, Ann Sarah, and Seale, Anna C.
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Infection -- Health aspects -- Analysis ,Health - Abstract
From identification of SARS-CoV-2 in December 2019 through September 22, 2022, [approximately equal to] 612 million confirmed cases and 6.5 million confirmed deaths were reported worldwide (1). During the COVID-19 [...]
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- 2023
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5. Diversity of symptom phenotypes in SARS-CoV-2 community infections observed in multiple large datasets
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Fyles, Martyn, Vihta, Karina-Doris, Sudre, Carole H, Long, Harry, Das, Rajenki, Jay, Caroline, Wingfield, Tom, Cumming, Fergus, Green, William, Hadjipantelis, Pantelis, Kirk, Joni, Steves, Claire J, Ourselin, Sebastien, Medley, Graham F, Fearon, Elizabeth, and House, Thomas
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Statistics - Applications ,Quantitative Biology - Populations and Evolution ,62P10 - Abstract
Through the use of cutting-edge unsupervised classification techniques from statistics and machine learning, we characterise symptom phenotypes among symptomatic SARS-CoV-2 PCR-positive community cases. We first analyse each dataset in isolation and across age bands, before using methods that allow us to compare multiple datasets. While we observe separation due to the total number of symptoms experienced by cases, we also see a separation of symptoms into gastrointestinal, respiratory and other types, and different symptom co-occurrence patterns at the extremes of age. In this way, we are able to demonstrate the deep structure of symptoms of COVID-19 without usual biases due to study design. This is expected to have implications for the identification and management of community SARS-CoV-2 cases and could be further applied to symptom-based management of other diseases and syndromes., Comment: 60 pages; 29 figures
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- 2021
6. Diversity of symptom phenotypes in SARS-CoV-2 community infections observed in multiple large datasets
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Fyles, Martyn, Vihta, Karina-Doris, Sudre, Carole H, Long, Harry, Das, Rajenki, Jay, Caroline, Wingfield, Tom, Cumming, Fergus, Green, William, Hadjipantelis, Pantelis, Kirk, Joni, Steves, Claire J, Ourselin, Sebastien, Medley, Graham F, Fearon, Elizabeth, and House, Thomas
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- 2023
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7. Using electronic health records to improve management of E. coli bloodstream infections
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Vihta, Karina-Doris, Walker, Ann Sarah, Crook, Derrick, Peto, Tim, and Eyre, David
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616.9 ,Whole genome sequencing ,Infections ,Epidemiology ,Antimicrobial resistance ,Machine learning ,Medical records--Data processing - Abstract
The aim of this thesis is to use linked electronic health records of hospital admissions, and microbiology and haematology results in order to inform management of infections in Oxfordshire, and more generally worldwide. Escherichia coli is one of the leading bacterial pathogens causing bloodstream infections; not only is overall incidence rising, but rising resistance to commonly used empiric antibiotics is also a major concern. Despite playing such a significant role in the burden of infections, the epidemiology of E. coli bloodstream infections is still unclear, particularly when considering unselected populations. I showed that the rise in E. coli bloodstream infections in Oxfordshire is driven by truly community-associated cases, that is, cases identified in the first 48 hours of a hospital admission, or outside of a hospital admission, who had not been admitted to the hospital in the past year. Interestingly, the rate of increase in incidence was faster the further away the previous hospital admission had been. However, rising incidence did not seem to be driven by increasing numbers of patients with evidence of a previous urinary tract infection. The number of co-amoxiclav resistant infections was rising significantly faster than the number of co-amoxiclav susceptible infections and the highest number of resistant infections in 2016 was seen in community-associated cases. However, considering 30-day mortality and various biomarkers of infection, there was no evidence for changes in the severity of infections over time. Higher co-amoxiclav use in primary care was associated with higher rates of co-amoxiclav resistant E. coli urinary tract infections in the subsequent year, providing the evidence needed in order to support the aim of lowering inappropriate use of broad-spectrum antibiotics in the community. Co-amoxiclav susceptibility is particularly challenging to define with traditional laboratory testing methods, with different methodologies leading to different results both in terms of minimum inhibitory concentrations, but particularly when considering a dichotomised susceptible/resistant phenotype. Recent advances in whole genome sequencing technology and analysis tools, as well as decreases in costs, increase the potential utility of predicting phenotype from sequencing-derived genotype, particularly for challenging bacteria-drug combinations. I found that machine learning algorithms – statistical methods which learn from patterns within the data without being programmed explicitly – could predict co-amoxiclav resistance where information is extracted from assembled sequences, either through extracting information about genetic features from mapping onto resistance databases or by considering presence and absence of DNA ‘words’ (k-mers). Crucially, feature selection and expert knowledge are not required when constructing these matrices of genetic features, making these algorithms particularly appealing when considering the constant accumulation of new genetic resistance mechanisms. Finally, by comparing the proportions of resistant bloodstream infections and infections in other less invasive sites, I found that the latter could be used as a surveillance tool for antimicrobial resistance in low- and middle-income countries, since these sites are easier to sample from and cheaper to carry out antimicrobial susceptibility testing on.
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- 2020
8. Detecting changes in population trends in infection surveillance using community SARS-CoV-2 prevalence as an exemplar
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Pritchard, Emma, primary, Vihta, Karina-Doris, additional, Eyre, David W, additional, Hopkins, Susan, additional, Peto, Tim E A, additional, Matthews, Philippa C, additional, Stoesser, Nicole, additional, Studley, Ruth, additional, Rourke, Emma, additional, Diamond, Ian, additional, Pouwels, Koen B, additional, Walker, Ann Sarah, additional, and Infection Survey Team, the COVID-19, additional
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- 2024
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9. Molecular epidemiology and antimicrobial resistance phenotype of paediatric bloodstream infections caused by Gram-negative bacteria
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Lipworth, Sam, Vihta, Karina-Doris, Davies, Tim, Wright, Sarah, Tabirao, Merline, Chau, Kevin, Vaughan, Alison, Kavanagh, James, Barker, Leanne, George, Sophie, Segal, Shelley, Paulus, Stephane, Barrett, Lucinda, Oakley, Sarah, Jeffery, Katie, Butcher, Lisa, Peto, Tim, Crook, Derrick, Walker, Sarah, Kadambari, Seilesh, and Stoesser, Nicole
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- 2022
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10. Effect of Delta variant on viral burden and vaccine effectiveness against new SARS-CoV-2 infections in the UK
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Pouwels, Koen B., Pritchard, Emma, Matthews, Philippa C., Stoesser, Nicole, Eyre, David W., Vihta, Karina-Doris, and House, Thomas
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Infection control -- Methods ,Viremia -- Measurement ,Biological sciences ,Health - Abstract
The effectiveness of the BNT162b2 and ChAdOx1 vaccines against new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections requires continuous re-evaluation, given the increasingly dominant B.1.617.2 (Delta) variant. In this study, we investigated the effectiveness of these vaccines in a large, community-based survey of randomly selected households across the United Kingdom. We found that the effectiveness of BNT162b2 and ChAdOx1 against infections (new polymerase chain reaction (PCR)-positive cases) with symptoms or high viral burden is reduced with the B.1.617.2 variant (absolute difference of 10-13% for BNT162b2 and 16% for ChAdOx1) compared to the B.1.1.7 (Alpha) variant. The effectiveness of two doses remains at least as great as protection afforded by prior natural infection. The dynamics of immunity after second doses differed significantly between BNT162b2 and ChAdOx1, with greater initial effectiveness against new PCR-positive cases but faster declines in protection against high viral burden and symptomatic infection with BNT162b2. There was no evidence that effectiveness varied by dosing interval, but protection was higher in vaccinated individuals after a prior infection and in younger adults. With B.1.617.2, infections occurring after two vaccinations had similar peak viral burden as those in unvaccinated individuals. SARS-CoV-2 vaccination still reduces new infections, but effectiveness and attenuation of peak viral burden are reduced with B.1.617.2. A large, community-based study in the United Kingdom indicates that the effectiveness of BNT162b2 and ChAdOx1 vaccines against SARS-CoV-2 infections with symptoms or high viral burden is reduced with the Delta variant compared to the Alpha variant., Author(s): Koen B. Pouwels [sup.1] [sup.2] , Emma Pritchard [sup.1] [sup.3] , Philippa C. Matthews [sup.3] [sup.4] [sup.5] , Nicole Stoesser [sup.1] [sup.3] [sup.4] [sup.5] , David W. Eyre [sup.1] [...]
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- 2021
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11. Impact of vaccination on new SARS-CoV-2 infections in the United Kingdom
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Pritchard, Emma, Matthews, Philippa C., Stoesser, Nicole, Eyre, David W., Gethings, Owen, Vihta, Karina-Doris, and Jones, Joel
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Vaccination -- Influence ,Biological sciences ,Health - Abstract
The effectiveness of COVID-19 vaccination in preventing new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in the general community is still unclear. Here, we used the Office for National Statistics COVID-19 Infection Survey--a large community-based survey of individuals living in randomly selected private households across the United Kingdom--to assess the effectiveness of the BNT162b2 (Pfizer-BioNTech) and ChAdOx1 nCoV-19 (Oxford-AstraZeneca; ChAdOx1) vaccines against any new SARS-CoV-2 PCR-positive tests, split according to self-reported symptoms, cycle threshold value ( Results from the Office of National Statistics COVID-19 Infection Survey in the United Kingdom demonstrate that the ChAdOx1 nCoV-19 and BNT162b2 vaccines reduce the incidence of new SARS-CoV-2 infections by up to 65% with a single dose and up to 80% after two doses, with no significant differences in efficacy observed between the two vaccines., Author(s): Emma Pritchard [sup.1] [sup.2] , Philippa C. Matthews [sup.1] [sup.3] [sup.4] , Nicole Stoesser [sup.1] [sup.2] [sup.3] [sup.4] , David W. Eyre [sup.2] [sup.3] [sup.4] [sup.5] , Owen Gethings [...]
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- 2021
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12. Community prevalence of SARS-CoV-2 in England from April to November, 2020: results from the ONS Coronavirus Infection Survey
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Pouwels, Koen B., Walker, A. Sarah, Crook, Derrick, Matthews, Philippa C., Peto, Tim, Pritchard, Emma, Stoesser, Nicole, Vihta, Karina-Doris, Howarth, Alison, Doherty, George, Kavanagh, James, Chau, Kevin K., Hatch, Stephanie B., Ebner, Daniel, Martins Ferreira, Lucas, Christott, Thomas, Marsden, Brian D., Dejnirattisai, Wanwisa, Mongkolsapaya, Juthathip, Hoosdally, Sarah, Cornall, Richard, Stuart, David I., Screaton, Gavin, Eyre, David, Bell, John, Cox, Stuart, Paddon, Kevin, James, Tim, House, Thomas, Newton, John N., Robotham, Julie V., Birrell, Paul, Jordan, Helena, Sheppard, Tim, Athey, Graham, Moody, Dan, Curry, Leigh, Brereton, Pamela, Hay, Jodie, Vansteenhouse, Harper, Bell, Iain, Diamond, Ian, Lambert, Alex, Benton, Pete, Rourke, Emma, Hawkes, Stacey, Henry, Sarah, Scruton, James, Stokes, Peter, Thomas, Tina, Allen, John, Black, Russell, Bovill, Heather, Braunholtz, David, Brown, Dominic, Collyer, Sarah, Crees, Megan, Daglish, Colin, Davies, Byron, Donnarumma, Hannah, Douglas-Mann, Julia, Felton, Antonio, Finselbach, Hannah, Fordham, Eleanor, Ipser, Alberta, Jenkins, Joe, Jones, Joel, Kent, Katherine, Kerai, Geeta, Lloyd, Lina, Masding, Victoria, Osborn, Ellie, Patel, Alpi, Pereira, Elizabeth, Pett, Tristan, Randall, Melissa, Reeve, Donna, Shah, Palvi, Snook, Ruth, Studley, Ruth, Sutherland, Esther, Swinn, Eliza, Thomas, Heledd, Tudor, Anna, Weston, Joshua, Leib, Shayla, Tierney, James, Farkas, Gabor, Cobb, Raf, Van Galen, Folkert, Compton, Lewis, Irving, James, Clarke, John, Mullis, Rachel, Ireland, Lorraine, Airimitoaie, Diana, Nash, Charlotte, Cox, Danielle, Fisher, Sarah, Moore, Zoe, McLean, James, Kerby, Matt, Pouwels, Koen B, Robotham, Julie V, Birrell, Paul J, Gelman, Andrew, Bowers, Nikola, Boreham, Ian, Lewis, James, Bell, John I, Newton, John N, Farrar, Jeremy, and Walker, Ann Sarah
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- 2021
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13. SARS-CoV-2, influenza A/B and respiratory syncytial virus positivity and association with influenza-like illness and self-reported symptoms, over the 2022/23 winter season in the UK: a longitudinal surveillance cohort
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Dietz, Elisabeth, primary, Pritchard, Emma Elizabeth, additional, Pouwels, Koen, additional, Ehsaan, Muhammad, additional, Blake, Joshua, additional, Gaughan, Charlotte, additional, Haduli, Eric, additional, Boothe, Hugh, additional, Vihta, Karina-Doris, additional, Peto, Tim, additional, Stoesser, Nicole, additional, Matthews, Philippa, additional, Taylor, Nick, additional, Diamond, Ian, additional, Studley, Ruth, additional, Rourke, Emma, additional, Birrell, Paul, additional, De Angelis, Daniela, additional, Fowler, Tom, additional, Watson, Conall, additional, Eyre, David W, additional, House, Thomas, additional, and Walker, Ann Sarah, additional
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- 2023
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14. Antimicrobial resistance in commensal opportunistic pathogens isolated from non-sterile sites can be an effective proxy for surveillance in bloodstream infections
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Vihta, Karina-Doris, Gordon, Nicola Claire, Stoesser, Nicole, Quan, T. Phuong, Tyrrell, Carina S. B., Vongsouvath, Manivanh, Ashley, Elizabeth A., Chansamouth, Vilada, Turner, Paul, Ling, Clare L., Eyre, David W., White, Nicholas J., Crook, Derrick, Peto, Tim E. A., and Walker, Ann Sarah
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- 2021
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15. Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK
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Lipworth, Samuel, Vihta, Karina-Doris, Chau, Kevin, Barker, Leanne, George, Sophie, Kavanagh, James, Davies, Timothy, Vaughan, Alison, Andersson, Monique, Jeffery, Katie, Oakley, Sarah, Morgan, Marcus, Hopkins, Susan, Peto, Timothy E. A., Crook, Derrick W., Walker, Ann Sarah, and Stoesser, Nicole
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- 2021
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16. Trends over time in Escherichia coli bloodstream infections, urinary tract infections, and antibiotic susceptibilities in Oxfordshire, UK, 1998–2016: a study of electronic health records
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Vihta, Karina-Doris, Stoesser, Nicole, Llewelyn, Martin J, Quan, T Phuong, Davies, Tim, Fawcett, Nicola J, Dunn, Laura, Jeffery, Katie, Butler, Chris C, Hayward, Gail, Andersson, Monique, Morgan, Marcus, Oakley, Sarah, Mason, Amy, Hopkins, Susan, Wyllie, David H, Crook, Derrick W, Wilcox, Mark H, Johnson, Alan P, Peto, Tim E A, and Walker, A Sarah
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- 2018
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17. High Rates of Human Fecal Carriage of mcr-1 –Positive Multidrug-Resistant Enterobacteriaceae Emerge in China in Association With Successful Plasmid Families
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Zhong, Lan-Lan, Phan, Hang T. T., Shen, Cong, Vihta, Karina-Doris, Sheppard, Anna E., Huang, Xi, Zeng, Kun-Jiao, Li, Hong-Yu, Zhang, Xue-Fei, Patil, Sandip, Crook, Derrick W., Walker, A. Sarah, Xing, Yong, Lin, Jia-lin, Feng, Lian-Qiang, Doi, Yohei, Xia, Yong, Stoesser, Nicole, and Tian, Guo-Bao
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- 2018
18. Omicron-associated changes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) symptoms in the United Kingdom
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Vihta, Karina-Doris, Pouwels, Koen B, Peto, Tim EA, Pritchard, Emma, House, Thomas, Studley, Ruth, Rourke, Emma, Cook, Duncan, Diamond, Ian, Crook, Derrick, Clifton, David A, Matthews, Philippa C, Stoesser, Nicole, Eyre, David W, Walkerand, Ann Sarah, and team, COVID-19 Infection Survey
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FOS: Clinical medicine ,Immunology ,Infectious Disease ,Genetics & Genomics - Abstract
BACKGROUND: The SARS-CoV-2 Delta variant has been replaced by the highly transmissible Omicron BA.1 variant, and subsequently by Omicron BA.2. It is important to understand how these changes in dominant variants affect reported symptoms, while also accounting for symptoms arising from other co-circulating respiratory viruses. METHODS: In a nationally representative UK community study, the COVID-19 Infection Survey, we investigated symptoms in PCR-positive infection episodes vs. PCR-negative study visits over calendar time, by age and vaccination status, comparing periods when the Delta, Omicron BA.1 and BA.2 variants were dominant. RESULTS: Between October-2020 and April-2022, 120,995 SARS-CoV-2 PCR-positive episodes occurred in 115,886 participants, with 70,683 (58%) reporting symptoms. The comparator comprised 4,766,366 PCR-negative study visits (483,894 participants); 203,422 (4%) reporting symptoms. Symptom reporting in PCR-positives varied over time, with a marked reduction in loss of taste/smell as Omicron BA.1 dominated, maintained with BA.2 (44%/45% 17 October 2021, 16%/13% 2 January 2022, 15%/12% 27 March 2022). Cough, fever, shortness of breath, myalgia, fatigue/weakness and headache also decreased after Omicron BA.1 dominated, but sore throat increased, the latter to a greater degree than concurrent increases in PCR-negatives. Fatigue/weakness increased again after BA.2 dominated, although to a similar degree to concurrent increases in PCR-negatives. Symptoms were consistently more common in adults aged 18-65 years than in children or older adults. CONCLUSIONS: Increases in sore throat (also common in the general community), and a marked reduction in loss of taste/smell, make Omicron harder to detect with symptom-based testing algorithms, with implications for institutional and national testing policies.
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- 2023
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19. COVID-19 vaccination, risk-compensatory behaviours, and contacts in the UK.
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Buckell, John, Jones, Joel, Matthews, Philippa C., Diamond, Sir Ian, Rourke, Emma, Studley, Ruth, Cook, Duncan, Walker, Ann Sarah, Pouwels, Koen B., the COVID-19 Infection Survey Team, Thomas, Tina, Ayoubkhani, Daniel, Black, Russell, Felton, Antonio, Crees, Megan, Lloyd, Lina, Sutherland, Esther, Pritchard, Emma, Vihta, Karina-Doris, and Doherty, George
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COVID-19 vaccines ,HAZARD mitigation ,VACCINATION ,SARS-CoV-2 - Abstract
The physiological effects of vaccination against SARS-CoV-2 (COVID-19) are well documented, yet the behavioural effects not well known. Risk compensation suggests that gains in personal safety, as a result of vaccination, are offset by increases in risky behaviour, such as socialising, commuting and working outside the home. This is potentially important because transmission of SARS-CoV-2 is driven by contacts, which could be amplified by vaccine-related risk compensation. Here, we show that behaviours were overall unrelated to personal vaccination, but—adjusting for variation in mitigation policies—were responsive to the level of vaccination in the wider population: individuals in the UK were risk compensating when rates of vaccination were rising. This effect was observed across four nations of the UK, each of which varied policies autonomously. [ABSTRACT FROM AUTHOR]
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- 2023
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20. Antibody responses and correlates of protection in the general population after two doses of the ChAdOx1 or BNT162b2 vaccines
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Wei, Jia, Pouwels, Koen B., Stoesser, Nicole, Matthews, Philippa C., Diamond, Ian, Studley, Ruth, Rourke, Emma, Cook, Duncan, Bell, John I., Newton, John N., Farrar, Jeremy, Howarth, Alison, Marsden, Brian D., Hoosdally, Sarah, Jones, E. Yvonne, Stuart, David I., Crook, Derrick W., Peto, Tim E. A., Walker, A. Sarah, Eyre, David W., Thomas, Tina, Ayoubkhani, Daniel, Black, Russell, Felton, Antonio, Crees, Megan, Jones, Joel, Lloyd, Lina, Sutherland, Esther, Pritchard, Emma, Vihta, Karina-Doris, Doherty, George, Kavanagh, James, Chau, Kevin K., Hatch, Stephanie B., Ebner, Daniel, Ferreira, Lucas Martins, Christott, Thomas, Dejnirattisai, Wanwisa, Mongkolsapaya, Juthathip, Cameron, Sarah, Tamblin-Hopper, Phoebe, Wolna, Magda, Brown, Rachael, Cornall, Richard, Screaton, Gavin, Lythgoe, Katrina, Bonsall, David, Golubchik, Tanya, Fryer, Helen, Cox, Stuart, Paddon, Kevin, James, Tim, House, Thomas, Robotham, Julie, Birrell, Paul, Jordan, Helena, Sheppard, Tim, Athey, Graham, Moody, Dan, Curry, Leigh, Brereton, Pamela, Jarvis, Ian, Godsmark, Anna, Morris, George, Mallick, Bobby, Eeles, Phil, Hay, Jodie, VanSteenhouse, Harper, Lee, Jessica, White, Sean, Evans, Tim, Bloemberg, Lisa, Allison, Katie, Pandya, Anouska, Davis, Sophie, Conway, David I., MacLeod, Margaret, and Cunningham, Chris
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Antibody responses are an important part of immunity after Coronavirus Disease 2019 (COVID-19) vaccination. However, antibody trajectories and the associated duration of protection after a second vaccine dose remain unclear. In this study, we investigated anti-spike IgG antibody responses and correlates of protection after second doses of ChAdOx1 or BNT162b2 vaccines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the United Kingdom general population. In 222,493 individuals, we found significant boosting of anti-spike IgG by the second doses of both vaccines in all ages and using different dosing intervals, including the 3-week interval for BNT162b2. After second vaccination, BNT162b2 generated higher peak levels than ChAdOX1. Older individuals and males had lower peak levels with BNT162b2 but not ChAdOx1, whereas declines were similar across ages and sexes with ChAdOX1 or BNT162b2. Prior infection significantly increased antibody peak level and half-life with both vaccines. Anti-spike IgG levels were associated with protection from infection after vaccination and, to an even greater degree, after prior infection. At least 67% protection against infection was estimated to last for 2–3 months after two ChAdOx1 doses, for 5–8 months after two BNT162b2 doses in those without prior infection and for 1–2 years for those unvaccinated after natural infection. A third booster dose might be needed, prioritized to ChAdOx1 recipients and those more clinically vulnerable.
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- 2022
21. The mobilome associated with Gram-negative bloodstream infections: A large-scale observational hybrid sequencing based study
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Lipworth, Samuel, primary, Matlock, Willam, additional, Shaw, Liam, additional, Vihta, Karina-Doris, additional, Rodger, Gillian, additional, Chau, Kevin, additional, Barker, Leanne, additional, George, Sophie, additional, Kavanagh, James, additional, Davies, Timothy, additional, Vaughan, Alison, additional, Andersson, Monique, additional, Jeffery, Katie, additional, Oakley, Sarah, additional, Morgan, Marcus, additional, Hopkins, Susan, additional, Peto, Timothy, additional, Crook, Derrick, additional, Walker, A. Sarah, additional, and Stoesser, Nicole, additional
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- 2022
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22. Monitoring populations at increased risk for SARS-CoV-2 infection in the community using population-level demographic and behavioural surveillance
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Pritchard, Emma, primary, Jones, Joel, additional, Vihta, Karina-Doris, additional, Stoesser, Nicole, additional, Matthews, Prof Philippa C., additional, Eyre, David W., additional, House, Thomas, additional, Bell, John I, additional, Newton, Prof John N, additional, Farrar, Jeremy, additional, Crook, Prof Derrick, additional, Hopkins, Susan, additional, Cook, Duncan, additional, Rourke, Emma, additional, Studley, Ruth, additional, Diamond, Prof Ian, additional, Peto, Prof Tim, additional, Pouwels, Koen B., additional, and Walker, Prof A. Sarah, additional
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- 2022
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23. Tracking the emergence of SARS-CoV-2 alpha variant in the United Kingdom
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Walker, A. Sarah, Vihta, Karina-Doris, Gethings, Owen, Pritchard, Emma, Jones, Joel, House, Thomas, Bell, Iain, Bell, John I., Newton, John N., Farrar, Jeremy, Diamond, Ian, Studley, Ruth, Rourke, Emma, Hay, Jodie, Hopkins, Susan, Crook, Derrick, Peto, Tim, Matthews, Philippa C., Eyre, David W., Stoesser, Nicole, Pouwels, Koen B., and Covid-19 Infection Survey Team
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0303 health sciences ,SARS-CoV-2 ,COVID-19 ,General Medicine ,Health Surveys ,Polymerase Chain Reaction ,United Kingdom ,03 medical and health sciences ,0302 clinical medicine ,Population Surveillance ,Correspondence ,Humans ,Longitudinal Studies ,030212 general & internal medicine ,030304 developmental biology - Abstract
No abstract available.
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- 2021
24. Symptoms and SARS-CoV-2 positivity in the general population in the UK
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Vihta, Karina-Doris, Pouwels, Koen B, Peto, Tim, Pritchard, Emma, Eyre, David W, House, Thomas, Gethings, Owen, Studley, Ruth, Rourke, Emma, Cook, Duncan, Diamond, Ian, Crook, Derrick, Matthews, Philippa C, Stoesser, Nicole, and Walker, Ann Sarah
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AcademicSubjects/MED00290 ,COVID-19 Testing ,Fever ,SARS-CoV-2 ,Major Article ,community ,symptoms ,COVID-19 ,Humans ,United Kingdom - Abstract
"Classic" symptoms (cough, fever, loss of taste/smell) prompt severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) polymerase chain reaction (PCR) testing in the United Kingdom. Studies have assessed the ability of different symptoms to identify infection, but few have compared symptoms over time (reflecting variants) and by vaccination status.Using the COVID-19 Infection Survey, sampling households across the United Kingdom, we compared symptoms in PCR-positives vs PCR-negatives, evaluating sensitivity of combinations of 12 symptoms (percentage symptomatic PCR-positives reporting specific symptoms) and tests per case (TPC) (PCR-positives or PCR-negatives reporting specific symptoms/ PCR-positives reporting specific symptoms).Between April 2020 and August 2021, 27 869 SARS-CoV-2 PCR-positive episodes occurred in 27 692 participants (median 42 years), of whom 13 427 (48%) self-reported symptoms ("symptomatic PCR-positives"). The comparator comprised 3 806 692 test-negative visits (457 215 participants); 130 612 (3%) self-reported symptoms ("symptomatic PCR-negatives"). Symptom reporting in PCR-positives varied by age, sex, and ethnicity, and over time, reflecting changes in prevalence of viral variants, incidental changes (eg, seasonal pathogens (with sore throat increasing in PCR-positives and PCR-negatives from April 2021), schools reopening) and vaccination rollout. After May 2021 when Delta emerged, headache and fever substantially increased in PCR-positives, but not PCR-negatives. Sensitivity of symptom-based detection increased from 74% using "classic" symptoms, to 81% adding fatigue/weakness, and 90% including all 8 additional symptoms. However, this increased TPC from 4.6 to 5.3 to 8.7.Expanded symptom combinations may provide modest benefits for sensitivity of PCR-based case detection, but this will vary between settings and over time, and increases tests/case. Large-scale changes to targeted PCR-testing approaches require careful evaluation given substantial resource and infrastructure implications.
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- 2021
25. Anti-spike antibody response to natural SARS-CoV-2 infection in the general population
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Wei, Jia, Matthews, Philippa C., Stoesser, Nicole, Maddox, Thomas, Lorenzi, Luke, Studley, Ruth, Bell, John I., Newton, John N., Farrar, Jeremy, Diamond, Ian, Rourke, Emma, Howarth, Alison, Marsden, Brian D., Hoosdally, Sarah, Jones, E. Yvonne, Stuart, David I., Crook, Derrick W., Peto, Tim E. A., Pouwels, Koen B., Walker, A. Sarah, Eyre, David W., Thomas, Tina, Cook, Duncan, Ayoubkhani, Daniel, Black, Russell, Felton, Antonio, Crees, Megan, Jones, Joel, Lloyd, Lina, Sutherland, Esther, Pritchard, Emma, Vihta, Karina-Doris, Doherty, George, Kavanagh, James, Chau, Kevin K., Hatch, Stephanie B., Ebner, Daniel, Ferreira, Lucas Martins, Christott, Thomas, Dejnirattisai, Wanwisa, Mongkolsapaya, Juthathip, Cameron, Sarah, Tamblin-Hopper, Phoebe, Wolna, Magda, Brown, Rachael, Cornall, Richard, Screaton, Gavin, Lythgoe, Katrina, Bonsall, David, Golubchik, Tanya, Fryer, Helen, Cox, Stuart, Paddon, Kevin, James, Tim, House, Thomas, Robotham, Julie, Birrell, Paul, Jordan, Helena, Sheppard, Tim, Athey, Graham, Moody, Dan, Curry, Leigh, Brereton, Pamela, Jarvis, Ian, Godsmark, Anna, Morris, George, Mallick, Bobby, Eeles, Phil, Hay, Jodie, VanSteenhouse, Harper, Lee, Jessica, White, Sean, Evans, Tim, Bloemberg, Lisa, Allison, Katie, Pandya, Anouska, Davis, Sophie, Conway, David I., MacLeod, Margaret, and Cunningham, Chris
- Abstract
Understanding the trajectory, duration, and determinants of antibody responses after SARS-CoV-2 infection can inform subsequent protection and risk of reinfection, however large-scale representative studies are limited. Here we estimated antibody response after SARS-CoV-2 infection in the general population using representative data from 7,256 United Kingdom COVID-19 infection survey participants who had positive swab SARS-CoV-2 PCR tests from 26-April-2020 to 14-June-2021. A latent class model classified 24% of participants as ‘non-responders’ not developing anti-spike antibodies, who were older, had higher SARS-CoV-2 cycle threshold values during infection (i.e. lower viral burden), and less frequently reported any symptoms. Among those who seroconverted, using Bayesian linear mixed models, the estimated anti-spike IgG peak level was 7.3-fold higher than the level previously associated with 50% protection against reinfection, with higher peak levels in older participants and those of non-white ethnicity. The estimated anti-spike IgG half-life was 184 days, being longer in females and those of white ethnicity. We estimated antibody levels associated with protection against reinfection likely last 1.5-2 years on average, with levels associated with protection from severe infection present for several years. These estimates could inform planning for vaccination booster strategies.
- Published
- 2021
26. Exploring temporal trends and risk factors for resistance in Escherichia coli-causing bacteraemia in England between 2013 and 2018: an ecological study
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Aliabadi, Shirin, primary, Jauneikaite, Elita, additional, Müller-Pebody, Berit, additional, Hope, Russell, additional, Vihta, Karina-Doris, additional, Horner, Carolyne, additional, and Costelloe, Céire E, additional
- Published
- 2021
- Full Text
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27. Antibody responses to SARS-CoV-2 vaccines in 45,965 adults from the general population of the United Kingdom
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Wei, Jia, Stoesser, Nicole, Matthews, Philippa C., Ayoubkhani, Daniel, Studley, Ruth, Bell, Iain, Bell, John I., Newton, John N., Farrar, Jeremy, Diamond, Ian, Rourke, Emma, Howarth, Alison, Marsden, Brian D., Hoosdally, Sarah, Jones, E. Yvonne, Stuart, David I., Crook, Derrick W., Peto, Tim E. A., Pouwels, Koen B., Eyre, David W., Walker, A. Sarah, Lambert, Alex, Thomas, Tina, Black, Russell, Felton, Antonio, Crees, Megan, Jones, Joel, Lloyd, Lina, Sutherland, Esther, Pritchard, Emma, Vihta, Karina-Doris, Doherty, George, Kavanagh, James, Chau, Kevin K., Hatch, Stephanie B., Ebner, Daniel, Ferreira, Lucas Martins, Christott, Thomas, Dejnirattisai, Wanwisa, Mongkolsapaya, Juthathip, Cameron, Sarah, Tamblin-Hopper, Phoebe, Wolna, Magda, Brown, Rachael, Cornall, Richard, Screaton, Gavin, Lythgoe, Katrina, Bonsall, David, Golubchik, Tanya, Fryer, Helen, Cox, Stuart, Paddon, Kevin, James, Tim, House, Thomas, Robotham, Julie, Birrell, Paul, Jordan, Helena, Sheppard, Tim, Athey, Graham, Moody, Dan, Curry, Leigh, Brereton, Pamela, Jarvis, Ian, Godsmark, Anna, Morris, George, Mallick, Bobby, Eeles, Phil, Hay, Jodie, VanSteenhouse, Harper, and Lee, Jessica
- Abstract
We report that in a cohort of 45,965 adults, who were receiving either the ChAdOx1 or the BNT162b2 SARS-CoV-2 vaccines, in those who had no prior infection with SARS-CoV-2, seroconversion rates and quantitative antibody levels after a single dose were lower in older individuals, especially in those aged >60 years. Two vaccine doses achieved high responses across all ages. Antibody levels increased more slowly and to lower levels with a single dose of ChAdOx1 compared with a single dose of BNT162b2, but waned following a single dose of BNT162b2 in older individuals. In descriptive latent class models, we identified four responder subgroups, including a ‘low responder’ group that more commonly consisted of people aged >75 years, males and individuals with long-term health conditions. Given our findings, we propose that available vaccines should be prioritized for those not previously infected and that second doses should be prioritized for individuals aged >60 years. Further data are needed to better understand the extent to which quantitative antibody responses are associated with vaccine-mediated protection.
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- 2021
28. Symptoms and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Positivity in the General Population in the United Kingdom.
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Vihta, Karina Doris, Pouwels, Koen B, Peto, Tim E A, Pritchard, Emma, Eyre, David W, House, Thomas, Gethings, Owen, Studley, Ruth, Rourke, Emma, Cook, Duncan, Diamond, Ian, Crook, Derrick, Matthews, Philippa C, Stoesser, Nicole, Walker, Ann Sarah, and Survey, COVID-19 Infection
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POPULATION , *COVID-19 , *FEVER , *SELF-evaluation , *COMPARATIVE studies , *DESCRIPTIVE statistics , *COVID-19 testing , *POLYMERASE chain reaction , *SENSITIVITY & specificity (Statistics) , *HEADACHE , *PHARYNGITIS - Abstract
Background "Classic" symptoms (cough, fever, loss of taste/smell) prompt severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) polymerase chain reaction (PCR) testing in the United Kingdom. Studies have assessed the ability of different symptoms to identify infection, but few have compared symptoms over time (reflecting variants) and by vaccination status. Methods Using the COVID-19 Infection Survey, sampling households across the United Kingdom, we compared symptoms in PCR-positives vs PCR-negatives, evaluating sensitivity of combinations of 12 symptoms (percentage symptomatic PCR-positives reporting specific symptoms) and tests per case (TPC) (PCR-positives or PCR-negatives reporting specific symptoms/ PCR-positives reporting specific symptoms). Results Between April 2020 and August 2021, 27 869 SARS-CoV-2 PCR-positive episodes occurred in 27 692 participants (median 42 years), of whom 13 427 (48%) self-reported symptoms ("symptomatic PCR-positives"). The comparator comprised 3 806 692 test-negative visits (457 215 participants); 130 612 (3%) self-reported symptoms ("symptomatic PCR-negatives"). Symptom reporting in PCR-positives varied by age, sex, and ethnicity, and over time, reflecting changes in prevalence of viral variants, incidental changes (eg, seasonal pathogens (with sore throat increasing in PCR-positives and PCR-negatives from April 2021), schools reopening) and vaccination rollout. After May 2021 when Delta emerged, headache and fever substantially increased in PCR-positives, but not PCR-negatives. Sensitivity of symptom-based detection increased from 74% using "classic" symptoms, to 81% adding fatigue/weakness, and 90% including all 8 additional symptoms. However, this increased TPC from 4.6 to 5.3 to 8.7. Conclusions Expanded symptom combinations may provide modest benefits for sensitivity of PCR-based case detection, but this will vary between settings and over time, and increases tests/case. Large-scale changes to targeted PCR-testing approaches require careful evaluation given substantial resource and infrastructure implications. [ABSTRACT FROM AUTHOR]
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- 2022
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29. Systematic Review of Wastewater Surveillance of Antimicrobial Resistance in Human Populations
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Chau, Kevin, primary, Barker, Leanne, additional, Budgell, Eric, additional, Vihta, Karina-doris, additional, Sims, Natalie, additional, Kasprzyk-Hordern, Barbara, additional, Harriss, Elinor, additional, Crook, Derrick, additional, Read, Daniel, additional, Walker, Sarah, additional, and Stoesser, Nicole, additional
- Published
- 2021
- Full Text
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30. Molecular epidemiology of paediatric bloodstream infections caused by Gram-negative bacteria in Oxfordshire, UK
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Lipworth, Sam, primary, Vihta, Karina-Doris, additional, Davies, Tim, additional, Wright, Sarah, additional, Tabirao, Merline, additional, Chau, Kevin, additional, Vaughan, Alison, additional, Kavanagh, James, additional, Barker, Leanne, additional, George, Sophie, additional, Segal, Shelley, additional, Paulus, Stephane, additional, Barrett, Lucinda, additional, Oakley, Sarah, additional, Jeffery, Katie, additional, Butcher, Lisa, additional, Peto, Tim, additional, Crook, Derrick, additional, Walker, Sarah, additional, Kadambari, Seilesh, additional, and Stoesser, Nicole, additional
- Published
- 2021
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31. Impact of vaccination on new SARS-CoV-2 infections in the UK
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Pritchard, Emma, primary, Matthews, Philippa C., additional, Stoesser, Nicole, additional, Eyre, David W., additional, Gethings, Owen, additional, Vihta, Karina-Doris, additional, Jones, Joel, additional, House, Thomas, additional, VanSteenHouse, Harper, additional, Bell, Iain, additional, Bell, John I, additional, Newton, John N, additional, Farrar, Jeremy, additional, Diamond, Ian, additional, Rourke, Emma, additional, Studley, Ruth, additional, Crook, Derrick, additional, Peto, Tim, additional, Walker, A. Sarah, additional, and Pouwels, Koen B., additional
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- 2021
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32. Ten Years of Population-Level Genomic Escherichia coli and Klebsiella pneumoniae Serotype Surveillance Informs Vaccine Development for Invasive Infections
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Lipworth, Samuel, primary, Vihta, Karina-Doris, additional, Chau, Kevin K, additional, Kavanagh, James, additional, Davies, Timothy, additional, George, Sophie, additional, Barker, Leanne, additional, Vaughan, Ali, additional, Andersson, Monique, additional, Jeffery, Katie, additional, Oakley, Sarah, additional, Morgan, Marcus, additional, Peto, Timothy E A, additional, Crook, Derrick W, additional, Walker, A Sarah, additional, and Stoesser, Nicole, additional
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- 2021
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33. Molecular epidemiology of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire (UK) 2008-2018
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Lipworth, Samuel, primary, Vihta, Karina-Doris, additional, Chau, Kevin, additional, Barker, Leanne, additional, George, Sophie, additional, Kavanagh, James, additional, Davies, Timothy, additional, Vaughan, Alison, additional, Andersson, Monique, additional, Jeffery, Katie, additional, Oakley, Sarah, additional, Morgan, Marcus, additional, Hopkins, Susan, additional, Peto, Timothy E. A., additional, Crook, Derrick W., additional, Walker, Ann Sarah, additional, and Stoesser, Nicole, additional
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- 2021
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34. Antimicrobial resistance surveillance: can we estimate resistance in bloodstream infections from other types of specimen?
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Vihta, Karina-Doris, primary, Gordon, Nicola Claire, additional, Stoesser, Nicole, additional, Quan, T. Phuong, additional, Tyrrell, Carina SB, additional, Vongsouvath, Manivanh, additional, Ashley, Elizabeth A, additional, Chansamouth, Vilada, additional, Turner, Paul, additional, Ling, Clare L, additional, Eyre, David, additional, White, Nicholas J, additional, Crook, Derrick, additional, Peto, Tim, additional, and Walker, Ann Sarah, additional
- Published
- 2020
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35. Exploring temporal trends and risk factors for resistance in Escherichia coli-causing bacteraemia in England between 2013 and 2018: an ecological study.
- Author
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Aliabadi, Shirin, Jauneikaite, Elita, Müller-Pebody, Berit, Hope, Russell, Vihta, Karina-Doris, Horner, Carolyne, and Costelloe, Céire E
- Subjects
MICROBIAL sensitivity tests ,ESCHERICHIA ,LOGISTIC regression analysis ,BACTEREMIA ,DRUG resistance in bacteria ,GRAM-negative bacteria - Abstract
Background: Escherichia coli are Gram-negative bacteria associated with an increasing burden of antimicrobial resistance (AMR) in England.Objectives: To create a comprehensive epidemiological picture of E. coli bacteraemia resistance trends and risk factors in England by linking national microbiology data sources and performing a longitudinal analysis of rates.Methods: A retrospective observational study was conducted on all national records for antimicrobial susceptibility testing on E. coli bacteraemia in England from 1 January 2013 to 31 December 2018 from the UK Health Security Agency (UKHSA) and the BSAC Resistance Surveillance Programme (BSAC-RSP). Trends in AMR and MDR were estimated using iterative sequential regression. Logistic regression analyses were performed on UKHSA data to estimate the relationship between risk factors and AMR or MDR in E. coli bacteraemia isolates.Results: An increase in resistance rates was observed in community- and hospital-onset bacteraemia for third-generation cephalosporins, co-amoxiclav, gentamicin and ciprofloxacin. Among community-acquired cases, and after adjustment for other factors, patients aged >65 years were more likely to be infected by E. coli isolates resistant to at least one of 11 antibiotics than those aged 18-64 years (OR: 1.21, 95% CI: 1.18-1.25; P < 0.05). In hospital-onset cases, E. coli isolates from those aged 1-17 years were more likely to be resistant than those aged 18-64 years (OR: 1.33, 95% CI: 1.02-1.73; P < 0.05).Conclusions: Antibiotic resistance rates in E. coli-causing bacteraemia increased between 2013 and 2018 in England for key antimicrobial agents. Findings of this study have implications for guiding future policies on a prescribing of antimicrobial agents, for specific patient populations in particular. [ABSTRACT FROM AUTHOR]- Published
- 2022
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36. Ten years of population-level genomic Escherichia coli and Klebsiella pneumoniae serotype surveillance informs vaccine development for invasive infections
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Lipworth, Samuel, primary, Vihta, Karina-Doris, additional, Chau, Kevin K, additional, Kavanagh, James, additional, Davies, Timothy, additional, George, Sophie, additional, Barker, Leanne, additional, Vaughan, Ali, additional, Andersson, Monique, additional, Jeffery, Katie, additional, Oakley, Sarah, additional, Morgan, Marcus, additional, Peto, Timothy EA, additional, Crook, Derrick W, additional, Walker, A Sarah, additional, and Stoesser, Nicole, additional
- Published
- 2020
- Full Text
- View/download PDF
37. Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time.
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Walker, A. Sarah, Pritchard, Emma, House, Thomas, Robotham, Julie V., Birrell, Paul J., Bell, Iain, Bell, John I., Newton, John N., Farrar, Jeremy, Diamond, Ian, Studley, Ruth, Hay, Jodie, Vihta, Karina-Doris, Peto, Timothy EA, Stoesser, Nicole, Matthews, Philippa C., Eyre, David W., and Pouwels, Koen B.
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- 2021
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38. Trends in Escherichia coli bloodstream infection, urinary tract infections and antibiotic susceptibilities in Oxfordshire, 1998-2016: an observational study
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Vihta, Karina-Doris, primary, Stoesser, Nicole, additional, Llewelyn, Martin J, additional, Quan, Phuong T, additional, Davies, Timothy, additional, Fawcett, Nicola, additional, Dunn, Laura, additional, Jeffery, Katie, additional, Butler, Christopher, additional, Hayward, Gail, additional, Andersson, Monique, additional, Morgan, Marcus, additional, Oakley, Sarah, additional, Mason, Amy, additional, Wyllie, David H, additional, Crook, Derrick, additional, Wilcox, Mark, additional, Johnson, Alan P, additional, Peto, Tim, additional, and Walker, Sarah A, additional
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- 2017
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39. High Rates of Human Fecal Carriage of mcr-1–Positive Multidrug-Resistant Enterobacteriaceae Emerge in China in Association With Successful Plasmid Families
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Zhong, Lan-Lan, primary, Phan, Hang T T, additional, Shen, Cong, additional, Vihta, Karina-Doris, additional, Sheppard, Anna E, additional, Huang, Xi, additional, Zeng, Kun-Jiao, additional, Li, Hong-Yu, additional, Zhang, Xue-Fei, additional, Patil, Sandip, additional, Crook, Derrick W, additional, Walker, A Sarah, additional, Xing, Yong, additional, Lin, Jia-lin, additional, Feng, Lian-Qiang, additional, Doi, Yohei, additional, Xia, Yong, additional, Stoesser, Nicole, additional, and Tian, Guo-Bao, additional
- Published
- 2017
- Full Text
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40. Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time
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Walker, A Sarah, Pritchard, Emma, House, Thomas, Robotham, Julie V, Birrell, Paul J, Bell, Iain, Bell, John I, Newton, John N, Farrar, Jeremy, Diamond, Ian, Studley, Ruth, Hay, Jodie, Vihta, Karina-Doris, Peto, Timothy Ea, Stoesser, Nicole, Matthews, Philippa C, Eyre, David W, Pouwels, Koen B, and COVID-19 Infection Survey Team
- Subjects
medicine ,COVID-19 Testing ,SARS-CoV-2 ,infectious disease ,microbiology ,community ,symptoms ,COVID-19 ,Humans ,Viral Load ,3. Good health - Abstract
BACKGROUND: Information on SARS-CoV-2 in representative community surveillance is limited, particularly cycle threshold (Ct) values (a proxy for viral load). METHODS: We included all positive nose and throat swabs 26 April 2020 to 13 March 2021 from the UK's national COVID-19 Infection Survey, tested by RT-PCR for the N, S, and ORF1ab genes. We investigated predictors of median Ct value using quantile regression. RESULTS: Of 3,312,159 nose and throat swabs, 27,902 (0.83%) were RT-PCR-positive, 10,317 (37%), 11,012 (40%), and 6550 (23%) for 3, 2, or 1 of the N, S, and ORF1ab genes, respectively, with median Ct = 29.2 (~215 copies/ml; IQR Ct = 21.9-32.8, 14-56,400 copies/ml). Independent predictors of lower Cts (i.e. higher viral load) included self-reported symptoms and more genes detected, with at most small effects of sex, ethnicity, and age. Single-gene positives almost invariably had Ct > 30, but Cts varied widely in triple-gene positives, including without symptoms. Population-level Cts changed over time, with declining Ct preceding increasing SARS-CoV-2 positivity. Of 6189 participants with IgG S-antibody tests post-first RT-PCR-positive, 4808 (78%) were ever antibody-positive; Cts were significantly higher in those remaining antibody negative. CONCLUSIONS: Marked variation in community SARS-CoV-2 Ct values suggests that they could be a useful epidemiological early-warning indicator. FUNDING: Department of Health and Social Care, National Institutes of Health Research, Huo Family Foundation, Medical Research Council UK; Wellcome Trust.
41. Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time
- Author
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Walker, A Sarah, Pritchard, Emma, House, Thomas, Robotham, Julie V, Birrell, Paul J, Bell, Iain, Bell, John I, Newton, John N, Farrar, Jeremy, Diamond, Ian, Studley, Ruth, Hay, Jodie, Vihta, Karina-Doris, Peto, Timothy EA, Stoesser, Nicole, Matthews, Philippa C, Eyre, David W, Pouwels, Koen B, and COVID-19 Infection Survey Team
- Subjects
Microbiology and Infectious Disease ,SARS-CoV-2 ,Medicine ,community ,symptoms ,Other ,3. Good health ,Research Article ,viral load - Abstract
Funder: Huo Family Foundation, Background:: Information on SARS-CoV-2 in representative community surveillance is limited, particularly cycle threshold (Ct) values (a proxy for viral load). Methods:: We included all positive nose and throat swabs 26 April 2020 to 13 March 2021 from the UK’s national COVID-19 Infection Survey, tested by RT-PCR for the N, S, and ORF1ab genes. We investigated predictors of median Ct value using quantile regression. Results:: Of 3,312,159 nose and throat swabs, 27,902 (0.83%) were RT-PCR-positive, 10,317 (37%), 11,012 (40%), and 6550 (23%) for 3, 2, or 1 of the N, S, and ORF1ab genes, respectively, with median Ct = 29.2 (~215 copies/ml; IQR Ct = 21.9–32.8, 14–56,400 copies/ml). Independent predictors of lower Cts (i.e. higher viral load) included self-reported symptoms and more genes detected, with at most small effects of sex, ethnicity, and age. Single-gene positives almost invariably had Ct > 30, but Cts varied widely in triple-gene positives, including without symptoms. Population-level Cts changed over time, with declining Ct preceding increasing SARS-CoV-2 positivity. Of 6189 participants with IgG S-antibody tests post-first RT-PCR-positive, 4808 (78%) were ever antibody-positive; Cts were significantly higher in those remaining antibody negative. Conclusions:: Marked variation in community SARS-CoV-2 Ct values suggests that they could be a useful epidemiological early-warning indicator. Funding:: Department of Health and Social Care, National Institutes of Health Research, Huo Family Foundation, Medical Research Council UK; Wellcome Trust.
42. Additional file 1 of Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK
- Author
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Lipworth, Samuel, Vihta, Karina-Doris, Chau, Kevin, Barker, Leanne, George, Sophie, Kavanagh, James, Davies, Timothy, Vaughan, Alison, Andersson, Monique, Jeffery, Katie, Oakley, Sarah, Morgan, Marcus, Hopkins, Susan, Peto, Timothy E. A., Crook, Derrick W., Walker, Ann Sarah, and Stoesser, Nicole
- Subjects
3. Good health - Abstract
Additional file 1: Fig S1. Gene presence/absence heatmap showing AMR gene presence/absence against the core genome phylogeny for E. coli. Fig S2: Time-scaled phylogenies for ST131, ST95, ST73 and ST69. Fig S3: Possible transmission within nursing homes. Fig S4: Gene presence/absence heatmap showing AMR gene presence/absence against the core genome phylogeny for Klebsiella spp. Fig S5: Manhattan plots of a pangenome wide association study of the association of genes with community/healthcare associated onset. Fig S6: Proportions of presumed infectious foci for CA and HA BSI. Fig S7: Timescaled phylogeny of Klebsiella pneumoniae ST490 with a heatmap of AMR genes. Fig S8: Phylogenetic tree of Klebsiella spp annotated with species and virulence score. Fig S9: top panel - plasmid types in the PlasmidFinder database identified in the major/other E. coli/Klebsiella spp., bottom left - plot showing kmer based plasmidome similarity (y-axis) against chromosome similarity (x-axis) for isolates of the same MLST. Fig S10: DAPC plots for Klebsiella spp. Fig S11: Networks of genes/plasmids/insertion sequences commonly co-occurring in E. coli. Fig S12: Networks of genes commonly co-occuring in Klebsiella spp. Table S1: Incidence rate ratios for sub-lineage of major STs identified by fastbaps. Table S2: SNP ratios (median within/between region) and (median HA/all) were calculated for each ST. Table S3: Evolutionary distinctiveness (ED) scores for community-associated (CA) and healthcare-associated (HA) isolates amongst major E. coli STs. Table S4: Top hits from a pangenome-wide association study (PGWAS) performed using Pyseer [50] of the assocation of gene presence/absence with pysician identified BSI source.
43. Additional file 1 of Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK
- Author
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Lipworth, Samuel, Vihta, Karina-Doris, Chau, Kevin, Barker, Leanne, George, Sophie, Kavanagh, James, Davies, Timothy, Vaughan, Alison, Andersson, Monique, Jeffery, Katie, Oakley, Sarah, Morgan, Marcus, Hopkins, Susan, Peto, Timothy E. A., Crook, Derrick W., Walker, Ann Sarah, and Stoesser, Nicole
- Subjects
3. Good health - Abstract
Additional file 1: Fig S1. Gene presence/absence heatmap showing AMR gene presence/absence against the core genome phylogeny for E. coli. Fig S2: Time-scaled phylogenies for ST131, ST95, ST73 and ST69. Fig S3: Possible transmission within nursing homes. Fig S4: Gene presence/absence heatmap showing AMR gene presence/absence against the core genome phylogeny for Klebsiella spp. Fig S5: Manhattan plots of a pangenome wide association study of the association of genes with community/healthcare associated onset. Fig S6: Proportions of presumed infectious foci for CA and HA BSI. Fig S7: Timescaled phylogeny of Klebsiella pneumoniae ST490 with a heatmap of AMR genes. Fig S8: Phylogenetic tree of Klebsiella spp annotated with species and virulence score. Fig S9: top panel - plasmid types in the PlasmidFinder database identified in the major/other E. coli/Klebsiella spp., bottom left - plot showing kmer based plasmidome similarity (y-axis) against chromosome similarity (x-axis) for isolates of the same MLST. Fig S10: DAPC plots for Klebsiella spp. Fig S11: Networks of genes/plasmids/insertion sequences commonly co-occurring in E. coli. Fig S12: Networks of genes commonly co-occuring in Klebsiella spp. Table S1: Incidence rate ratios for sub-lineage of major STs identified by fastbaps. Table S2: SNP ratios (median within/between region) and (median HA/all) were calculated for each ST. Table S3: Evolutionary distinctiveness (ED) scores for community-associated (CA) and healthcare-associated (HA) isolates amongst major E. coli STs. Table S4: Top hits from a pangenome-wide association study (PGWAS) performed using Pyseer [50] of the assocation of gene presence/absence with pysician identified BSI source.
44. Trends over time in Escherichia coli bloodstream infections, urinary tract infections, and antibiotic susceptibilities in Oxfordshire, UK, 1998-2016: a study of electronic health records.
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Stoesser, Nicole, Fawcett, Nicola J, Mason, Amy, Wyllie, David H, Vihta, Karina-Doris, Quan, T Phuong, Davies, Tim, Peto, Tim E A, Walker, A Sarah, Crook, Derrick W, Johnson, Alan P, Llewelyn, Martin J, Dunn, Laura, Jeffery, Katie, Andersson, Monique, Morgan, Marcus, Oakley, Sarah, Butler, Chris C, Hayward, Gail, and Hopkins, Susan
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ESCHERICHIA coli , *PUBLIC health , *REGRESSION analysis , *PATIENTS , *ANTIBIOTICS , *BACTEREMIA , *RESEARCH , *URINARY tract infections , *TIME , *RESEARCH methodology , *DISEASE incidence , *EVALUATION research , *MEDICAL cooperation , *COMPARATIVE studies , *ESCHERICHIA coli diseases , *DRUG resistance in microorganisms , *ENZYME inhibitors - Abstract
Background: Escherichia coli bloodstream infections are increasing in the UK and internationally. The evidence base to guide interventions against this major public health concern is small. We aimed to investigate possible drivers of changes in the incidence of E coli bloodstream infection and antibiotic susceptibilities in Oxfordshire, UK, over the past two decades, while stratifying for time since hospital exposure.Methods: In this observational study, we used all available data on E coli bloodstream infections and E coli urinary tract infections (UTIs) from one UK region (Oxfordshire) using anonymised linked microbiological data and hospital electronic health records from the Infections in Oxfordshire Research Database (IORD). We estimated the incidence of infections across a two decade period and the annual incidence rate ratio (aIRR) in 2016. We modelled the data using negative binomial regression on the basis of microbiological, clinical, and health-care-exposure risk factors. We investigated infection severity, 30-day all-cause mortality, and community and hospital amoxicillin plus clavulanic acid (co-amoxiclav) use to estimate changes in bacterial virulence and the effect of antimicrobial resistance on incidence.Findings: From Jan 1, 1998, to Dec 31, 2016, 5706 E coli bloodstream infections occurred in 5215 patients, and 228 376 E coli UTIs occurred in 137 075 patients. 1365 (24%) E coli bloodstream infections were nosocomial (onset >48 h after hospital admission), 1132 (20%) were quasi-nosocomial (≤30 days after discharge), 1346 (24%) were quasi-community (31-365 days after discharge), and 1863 (33%) were community (>365 days after hospital discharge). The overall incidence increased year on year (aIRR 1·06, 95% CI 1·05-1·06). In 2016, 212 (41%) of 515 E coli bloodstream infections and 3921 (28%) of 13 792 E coli UTIs were co-amoxiclav resistant. Increases in E coli bloodstream infections were driven by increases in community (aIRR 1·10, 95% CI 1·07-1·13; p<0·0001) and quasi-community (aIRR 1·08, 1·07-1·10; p<0·0001) cases. 30-day mortality associated with E coli bloodstream infection decreased over time in the nosocomial (adjusted rate ratio [RR] 0·98, 95% CI 0·96-1·00; p=0·03) group, and remained stable in the quasi-nosocomial (adjusted RR 0·98, 0·95-1·00; p=0·06), quasi-community (adjusted RR 0·99, 0·96-1·01; p=0·32), and community (adjusted RR 0·99, 0·96-1·01; p=0·21) groups. Mortality was, however, substantial at 14-25% across all hospital-exposure groups. Co-amoxiclav-resistant E coli bloodstream infections increased in all groups across the study period (by 11-18% per year, significantly faster than co-amoxiclav-susceptible E coli bloodstream infections; pheterogeneity<0·0001), as did co-amoxiclav-resistant E coli UTIs (by 14-29% per year; pheterogeneity<0·0001). Previous year co-amoxiclav use in primary-care facilities was associated with increased subsequent year community co-amoxiclav-resistant E coli UTIs (p=0·003).Interpretation: Increases in E coli bloodstream infections in Oxfordshire are primarily community associated, with substantial co-amoxiclav resistance; nevertheless, we found little or no change in mortality. Focusing interventions on primary care facilities, particularly those with high co-amoxiclav use, could be effective in reducing the incidence of co-amoxiclav-resistant E coli bloodstream infections, in this region and more generally.Funding: National Institute for Health Research. [ABSTRACT FROM AUTHOR]- Published
- 2018
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45. Omicron-associated changes in SARS-CoV-2 symptoms in the United Kingdom.
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Vihta KD, Pouwels KB, Peto TE, Pritchard E, House T, Studley R, Rourke E, Cook D, Diamond I, Crook D, Clifton DA, Matthews PC, Stoesser N, Eyre DW, and Walker AS
- Abstract
Background: The SARS-CoV-2 Delta variant has been replaced by the highly transmissible Omicron BA.1 variant, and subsequently by Omicron BA.2. It is important to understand how these changes in dominant variants affect reported symptoms, while also accounting for symptoms arising from other co-circulating respiratory viruses., Methods: In a nationally representative UK community study, the COVID-19 Infection Survey, we investigated symptoms in PCR-positive infection episodes vs. PCR-negative study visits over calendar time, by age and vaccination status, comparing periods when the Delta, Omicron BA.1 and BA.2 variants were dominant., Results: Between October-2020 and April-2022, 120,995 SARS-CoV-2 PCR-positive episodes occurred in 115,886 participants, with 70,683 (58%) reporting symptoms. The comparator comprised 4,766,366 PCR-negative study visits (483,894 participants); 203,422 (4%) reporting symptoms. Symptom reporting in PCR-positives varied over time, with a marked reduction in loss of taste/smell as Omicron BA.1 dominated, maintained with BA.2 (44%/45% 17 October 2021, 16%/13% 2 January 2022, 15%/12% 27 March 2022). Cough, fever, shortness of breath, myalgia, fatigue/weakness and headache also decreased after Omicron BA.1 dominated, but sore throat increased, the latter to a greater degree than concurrent increases in PCR-negatives. Fatigue/weakness increased again after BA.2 dominated, although to a similar degree to concurrent increases in PCR-negatives. Symptoms were consistently more common in adults aged 18-65 years than in children or older adults., Conclusions: Increases in sore throat (also common in the general community), and a marked reduction in loss of taste/smell, make Omicron harder to detect with symptom-based testing algorithms, with implications for institutional and national testing policies., (© The Author(s) 2022. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)
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- 2022
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46. Monitoring populations at increased risk for SARS-CoV-2 infection in the community using population-level demographic and behavioural surveillance.
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Pritchard E, Jones J, Vihta KD, Stoesser N, Matthews PPC, Eyre DW, House T, Bell JI, Newton PJN, Farrar J, Crook PD, Hopkins S, Cook D, Rourke E, Studley R, Diamond PI, Peto PT, Pouwels KB, and Walker PAS
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Background: The COVID-19 pandemic is rapidly evolving, with emerging variants and fluctuating control policies. Real-time population screening and identification of groups in whom positivity is highest could help monitor spread and inform public health messaging and strategy., Methods: To develop a real-time screening process, we included results from nose and throat swabs and questionnaires taken 19 July 2020-17 July 2021 in the UK's national COVID-19 Infection Survey. Fortnightly, associations between SARS-CoV-2 positivity and 60 demographic and behavioural characteristics were estimated using logistic regression models adjusted for potential confounders, considering multiple testing, collinearity, and reverse causality., Findings: Of 4,091,537 RT-PCR results from 482,677 individuals, 29,903 (0·73%) were positive. As positivity rose September-November 2020, rates were independently higher in younger ages, and those living in Northern England, major urban conurbations, more deprived areas, and larger households. Rates were also higher in those returning from abroad, and working in healthcare or outside of home. When positivity peaked December 2020-January 2021 (Alpha), high positivity shifted to southern geographical regions. With national vaccine roll-out from December 2020, positivity reduced in vaccinated individuals. Associations attenuated as rates decreased between February-May 2021. Rising positivity rates in June-July 2021 (Delta) were independently higher in younger, male, and unvaccinated groups. Few factors were consistently associated with positivity. 25/45 (56%) confirmed associations would have been detected later using 28-day rather than 14-day periods., Interpretation: Population-level demographic and behavioural surveillance can be a valuable tool in identifying the varying characteristics driving current SARS-CoV-2 positivity, allowing monitoring to inform public health policy., Funding: Department of Health and Social Care (UK), Welsh Government, Department of Health (on behalf of the Northern Ireland Government), Scottish Government, National Institute for Health Research., Competing Interests: DWE declares lecture fees from Gilead outside the submitted work. DC is a committee member for the International Development Section of the Royal Statistical Society, and a trustee for the Carers’ Hub Lambeth charity. No other author has a conflict of interest to declare., (© 2021 The Author(s).)
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- 2022
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47. Tracking the Emergence of SARS-CoV-2 Alpha Variant in the United Kingdom.
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Walker AS, Vihta KD, Gethings O, Pritchard E, Jones J, House T, Bell I, Bell JI, Newton JN, Farrar J, Diamond I, Studley R, Rourke E, Hay J, Hopkins S, Crook D, Peto T, Matthews PC, Eyre DW, Stoesser N, and Pouwels KB
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- COVID-19 epidemiology, COVID-19 transmission, Health Surveys, Humans, Longitudinal Studies, Polymerase Chain Reaction, Population Surveillance, United Kingdom epidemiology, COVID-19 virology, SARS-CoV-2 genetics
- Published
- 2021
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