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  1. Article ; Online: The effectiveness and efficiency of asymptomatic SARS-CoV-2 testing strategies for patient and healthcare workers within acute NHS hospitals during an omicron-like period.

    Evans, Stephanie / Naylor, Nichola R / Fowler, Tom / Hopkins, Susan / Robotham, Julie

    BMC infectious diseases

    2024  Volume 24, Issue 1, Page(s) 64

    Abstract: Background: Asymptomatic SARS-CoV-2 testing of hospitalised patients began in April-2020, with twice weekly healthcare worker (HCW) testing introduced in November-2020. Guidance recommending asymptomatic testing was withdrawn in August-2022. Assessing ... ...

    Abstract Background: Asymptomatic SARS-CoV-2 testing of hospitalised patients began in April-2020, with twice weekly healthcare worker (HCW) testing introduced in November-2020. Guidance recommending asymptomatic testing was withdrawn in August-2022. Assessing the impact of this decision from data alone is challenging due to concurrent changes in infection prevention and control practices, community transmission rates, and a reduction in ascertainment rate from reduced testing. Computational modelling is an effective tool for estimating the impact of this change.
    Methods: Using a computational model of SARS-CoV-2 transmission in an English hospital we estimate the effectiveness of several asymptomatic testing strategies, namely; (1) Symptomatic testing of patients and HCWs, (2) testing of all patients on admission with/without repeat testing on days 3 and 5-7, and (3) symptomatic testing plus twice weekly asymptomatic HCW testing with 70% compliance. We estimate the number of patient and HCW infections, HCW absences, number of tests, and tests per case averted or absence avoided, with differing community prevalence rates over a 12-week period.
    Results: Testing asymptomatic patients on admission reduces the rate of nosocomial SARS-CoV-2 infection by 8.1-21.5%. Additional testing at days 3 and 5-7 post admission does not significantly reduce infection rates. Twice weekly asymptomatic HCW testing can reduce the proportion of HCWs infected by 1.0-4.4% and monthly absences by 0.4-0.8%. Testing asymptomatic patients repeatedly requires up to 5.5 million patient tests over the period, and twice weekly asymptomatic HCW testing increases the total tests to almost 30 million. The most efficient patient testing strategy (in terms of tests required to prevent a single patient infection) was testing asymptomatic patients on admission across all prevalence levels. The least efficient was repeated testing of patients with twice weekly asymptomatic HCW testing in a low prevalence scenario, and in all other prevalence levels symptomatic patient testing with regular HCW testing was least efficient.
    Conclusions: Testing patients on admission can reduce the rate of nosocomial SARS-CoV-2 infection but there is little benefit of additional post-admission testing. Asymptomatic HCW testing has little incremental benefit for reducing patient cases at low prevalence but has a potential role at higher prevalence or with low community transmission. A full health-economic evaluation is required to determine the cost-effectiveness of these strategies.
    MeSH term(s) Humans ; COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19 Testing ; SARS-CoV-2 ; State Medicine ; Health Personnel ; Hospitals ; Cross Infection/diagnosis ; Cross Infection/prevention & control
    Language English
    Publishing date 2024-01-08
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041550-3
    ISSN 1471-2334 ; 1471-2334
    ISSN (online) 1471-2334
    ISSN 1471-2334
    DOI 10.1186/s12879-023-08948-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A self-controlled case series study to measure the risk of SARS-CoV-2 infection associated with attendance at sporting and cultural events: the UK Events Research Programme events.

    Douglas, Ian J / Peh, Jerlyn / Mansfield, Kathryn E / Trelfa, Anna / Fowler, Tom / Boulter, Matthew / Cleary, Paul / Smith, Jenifer / Edmunds, W John

    BMC medicine

    2024  Volume 22, Issue 1, Page(s) 100

    Abstract: Background: In 2021, whilst societies were emerging from major social restrictions during the SARS-CoV-2 pandemic, the UK government instigated an Events Research Programme to examine the risk of COVID-19 transmission from attendance at cultural events ... ...

    Abstract Background: In 2021, whilst societies were emerging from major social restrictions during the SARS-CoV-2 pandemic, the UK government instigated an Events Research Programme to examine the risk of COVID-19 transmission from attendance at cultural events and explore ways to enable people to attend a range of events whilst minimising risk of transmission. We aimed to measure any impact on risk of COVID-19 transmission from attendance at events held at or close to commercially viable capacity using routinely collected data.
    Methods: Data were obtained on attendees at Phase 3 Events Research Programme events, for which some infection risk mitigation measures were in place (i.e. evidence of vaccination or a negative lateral flow test). Attendance data were linked with COVID-19 test result data from the UK Test and Trace system. Using a self-controlled case series design, we measured the within person incidence rate ratio for testing positive for COVID-19, comparing the rate in days 3 to 9 following event attendance (high risk period) with days 1 and 2 and 10-16 (baseline period). Rate ratios were adjusted for estimates of underlying regional COVID-19 prevalence to account for population level fluctuations in infection risk, and events were grouped into broadly similar types.
    Results: From attendance data available for 188,851 attendees, 3357 people tested positive for COVID-19 during the observation period. After accounting for total testing trends over the period, incidence rate ratios and 95% confidence intervals for positive tests were 1.16 (0.53-2.57) for indoor seated events, 1.12 (0.95-1.30) for mainly outdoor seated events, 0.65 (0.51-0.83) for mainly outdoor partially seated events, and 1.70 (1.52-1.89) for mainly outdoor unseated multi-day events.
    Conclusions: For the majority of event types studied in the third phase of the UK Events Research Programme, we found no evidence of an increased risk of COVID-19 transmission associated with event attendance. However, we found a 70% increased risk of infection associated with attendance at mainly outdoor unseated multi-day events. We have also demonstrated a novel use for self-controlled case series methodology in monitoring infection risk associated with event attendance.
    MeSH term(s) Humans ; COVID-19/diagnosis ; COVID-19/epidemiology ; SARS-CoV-2 ; Pandemics ; Research ; United Kingdom/epidemiology
    Language English
    Publishing date 2024-03-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 2131669-7
    ISSN 1741-7015 ; 1741-7015
    ISSN (online) 1741-7015
    ISSN 1741-7015
    DOI 10.1186/s12916-024-03276-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The evaluation of a multi-day testing approach with antigen lateral flow devices for people eligible for community-based COVID-19 treatments.

    Fowler, Tom / Fellows, Alasdair / MacISaac, Rachael / Kolade, Olumide / Singh, Bhupinder / Eccles, Adam / Blandford, Edward / Tunkel, Sarah A

    The Journal of antimicrobial chemotherapy

    2023  Volume 78, Issue Suppl 2, Page(s) ii12–ii17

    Abstract: Background: COVID-19 therapeutics including antiviral and monoclonal antibody treatments (hereafter 'COVID-19 treatments') require rapid administration to be effective. As part of the community-based antiviral and therapeutic treatment pathway for COVID- ...

    Abstract Background: COVID-19 therapeutics including antiviral and monoclonal antibody treatments (hereafter 'COVID-19 treatments') require rapid administration to be effective. As part of the community-based antiviral and therapeutic treatment pathway for COVID-19 there has been a move from PCR testing in those eligible to a rapid antigen lateral flow testing regime.
    Objectives: To determine whether a multi-day lateral flow device (LFD) testing regime is a feasible alternative to PCR for diagnosing symptomatic patients eligible for COVID-19 treatments. An LFD regime might return a positive result more quickly than a PCR and hence expedite access to COVID-19 treatments.
    Methods: A retrospective analysis was conducted of diagnostic testing for SARS-CoV-2 with a combination of PCR and LFDs of symptomatic patients eligible for COVID-19 treatments. LFD testing patterns were not assigned. Patients self-censored and the patterns were retro-fitted to the observed results.
    Results: The LFD testing patterns offered high sensitivity, close to 92%; however, the false positive rate also increased, with most of the multi-day testing patterns having a false positive rate greater than 3%. The highest sensitivity was seen among patients who tested with LFD on the same day as PCR.
    Conclusions: There were multiple observed testing behaviours. We conclude that multi-day LFD testing for COVID-19 provides a feasible alternative to PCR to in eligible patients, allowing swift prescription of COVID-19 treatments in most cases. This approach requires acceptance of a trade-off for a small increase in false-positive and -negative results.
    MeSH term(s) Humans ; COVID-19/diagnosis ; SARS-CoV-2 ; COVID-19 Drug Treatment ; COVID-19 Testing ; Retrospective Studies ; Antiviral Agents/therapeutic use ; Sensitivity and Specificity
    Chemical Substances Antiviral Agents
    Language English
    Publishing date 2023-11-23
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 191709-2
    ISSN 1460-2091 ; 0305-7453
    ISSN (online) 1460-2091
    ISSN 0305-7453
    DOI 10.1093/jac/dkad313
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Genomic medicine: time for health-care transformation.

    Scott, Richard H / Fowler, Tom A / Caulfield, Mark

    Lancet (London, England)

    2019  Volume 394, Issue 10197, Page(s) 454–456

    MeSH term(s) Early Diagnosis ; Genomics/methods ; Humans ; Precision Medicine/methods ; Translational Medical Research
    Language English
    Publishing date 2019-08-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 3306-6
    ISSN 1474-547X ; 0023-7507 ; 0140-6736
    ISSN (online) 1474-547X
    ISSN 0023-7507 ; 0140-6736
    DOI 10.1016/S0140-6736(19)31796-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Effect of Covid-19 Vaccination on Transmission of Alpha and Delta Variants.

    Eyre, David W / Taylor, Donald / Purver, Mark / Chapman, David / Fowler, Tom / Pouwels, Koen B / Walker, A Sarah / Peto, Tim E A

    The New England journal of medicine

    2022  Volume 386, Issue 8, Page(s) 744–756

    Abstract: Background: Before the emergence of the B.1.617.2 (delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), vaccination reduced transmission of SARS-CoV-2 from vaccinated persons who became infected, potentially by reducing viral ... ...

    Abstract Background: Before the emergence of the B.1.617.2 (delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), vaccination reduced transmission of SARS-CoV-2 from vaccinated persons who became infected, potentially by reducing viral loads. Although vaccination still lowers the risk of infection, similar viral loads in vaccinated and unvaccinated persons who are infected with the delta variant call into question the degree to which vaccination prevents transmission.
    Methods: We used contact-testing data from England to perform a retrospective observational cohort study involving adult contacts of SARS-CoV-2-infected adult index patients. We used multivariable Poisson regression to investigate associations between transmission and the vaccination status of index patients and contacts and to determine how these associations varied with the B.1.1.7 (alpha) and delta variants and time since the second vaccination.
    Results: Among 146,243 tested contacts of 108,498 index patients, 54,667 (37%) had positive SARS-CoV-2 polymerase-chain-reaction (PCR) tests. In index patients who became infected with the alpha variant, two vaccinations with either BNT162b2 or ChAdOx1 nCoV-19 (also known as AZD1222), as compared with no vaccination, were independently associated with reduced PCR positivity in contacts (adjusted rate ratio with BNT162b2, 0.32; 95% confidence interval [CI], 0.21 to 0.48; and with ChAdOx1 nCoV-19, 0.48; 95% CI, 0.30 to 0.78). Vaccine-associated reductions in transmission of the delta variant were smaller than those with the alpha variant, and reductions in transmission of the delta variant after two BNT162b2 vaccinations were greater (adjusted rate ratio for the comparison with no vaccination, 0.50; 95% CI, 0.39 to 0.65) than after two ChAdOx1 nCoV-19 vaccinations (adjusted rate ratio, 0.76; 95% CI, 0.70 to 0.82). Variation in cycle-threshold (Ct) values (indicative of viral load) in index patients explained 7 to 23% of vaccine-associated reductions in transmission of the two variants. The reductions in transmission of the delta variant declined over time after the second vaccination, reaching levels that were similar to those in unvaccinated persons by 12 weeks in index patients who had received ChAdOx1 nCoV-19 and attenuating substantially in those who had received BNT162b2. Protection in contacts also declined in the 3-month period after the second vaccination.
    Conclusions: Vaccination was associated with a smaller reduction in transmission of the delta variant than of the alpha variant, and the effects of vaccination decreased over time. PCR Ct values at diagnosis of the index patient only partially explained decreased transmission. (Funded by the U.K. Government Department of Health and Social Care and others.).
    MeSH term(s) Adult ; Aged ; Aged, 80 and over ; BNT162 Vaccine ; COVID-19/diagnosis ; COVID-19/transmission ; COVID-19/virology ; COVID-19 Nucleic Acid Testing ; ChAdOx1 nCoV-19 ; Disease Transmission, Infectious/prevention & control ; England ; Female ; Humans ; Male ; Middle Aged ; Retrospective Studies ; SARS-CoV-2 ; Viral Load
    Chemical Substances ChAdOx1 nCoV-19 (B5S3K2V0G8) ; BNT162 Vaccine (N38TVC63NU)
    Language English
    Publishing date 2022-01-05
    Publishing country United States
    Document type Journal Article ; Observational Study ; Research Support, Non-U.S. Gov't
    ZDB-ID 207154-x
    ISSN 1533-4406 ; 0028-4793
    ISSN (online) 1533-4406
    ISSN 0028-4793
    DOI 10.1056/NEJMoa2116597
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Rapid antigen testing for SARS-CoV-2 by lateral flow assay: A field evaluation of self- and professional testing at UK community testing sites.

    Futschik, Matthias E / Johnson, Samuel / Turek, Elena / Chapman, David / Carr, Simon / Thorlu-Bangura, Zareen / Klapper, Paul E / Sudhanva, Malur / Dodgson, Andrew / Cole-Hamilton, Joanna R / Germanacos, Nick / Kulasegaran-Shylini, Raghavendran / Blandford, Edward / Tunkel, Sarah / Peto, Timothy / Hopkins, Susan / Fowler, Tom

    Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

    2024  Volume 171, Page(s) 105654

    Abstract: Background: The advent of lateral flow devices (LFDs) for SARS-CoV-2 detection enabled widespread use of rapid self-tests during the pandemic. While self-testing using LFDs is now common, whether self-testing provides comparable performance to ... ...

    Abstract Background: The advent of lateral flow devices (LFDs) for SARS-CoV-2 detection enabled widespread use of rapid self-tests during the pandemic. While self-testing using LFDs is now common, whether self-testing provides comparable performance to professional testing was a key question that remained important for pandemic planning.
    Methods: Three prospective multi-centre studies were conducted to compare the performance of self- and professional testing using LFDs. Participants tested themselves or were tested by trained (professional) testers at community testing sites in the UK. Corresponding qRT-PCR test results served as reference standard. The performance of Innova, Orient Gene and SureScreen LFDs by users (self) and professional testers was assessed in terms of sensitivity, specificity, and kit failure (void) rates. Impact of age, sex and symptom status was analysed using logistic regression modelling.
    Results: 16,617 participants provided paired tests, of which 15,418 were included in the analysis. Self-testing with Innova, Orient Gene or SureScreen LFDs achieved sensitivities of 50 %, 53 % or 72 %, respectively, compared to qRT-PCR. Self and professional LFD testing showed no statistically different sensitivity with respect to corresponding qRT-PCR testing. Specificity was consistently equal to or higher than 99 %. Sex and age had no or only marginal impact on LFD performance while sensitivity was significantly higher for symptomatic individuals. Sensitivity of LFDs increased strongly to up to 90 % with higher levels of viral RNA measured by qRT-PCR.
    Conclusions: Our results support SARS-CoV-2 self-testing with LFDs, especially for the detection of individuals whose qRT-PCR tests showed high viral concentrations.
    MeSH term(s) Humans ; COVID-19/diagnosis ; Prospective Studies ; SARS-CoV-2 ; Immunologic Tests ; United Kingdom ; Sensitivity and Specificity
    Language English
    Publishing date 2024-02-15
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1446080-4
    ISSN 1873-5967 ; 1386-6532
    ISSN (online) 1873-5967
    ISSN 1386-6532
    DOI 10.1016/j.jcv.2024.105654
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  7. Article ; Online: Faster detection of asymptomatic COVID-19 cases among care home staff in England through the combination of SARS-CoV-2 testing technologies.

    Ryan, Finola / Cole-Hamilton, Joanna / Dandamudi, Niharika / Futschik, Matthias E / Needham, Alexander / Saquib, Rida / Kulasegaran-Shylini, Raghavendran / Blandford, Edward / Kidd, Michael / O'Moore, Éamonn / Hall, Ian / Sudhanva, Malur / Klapper, Paul / Dodgson, Andrew / Moore, Adam / Duke, Madeleine / Tunkel, Sarah / Kenny, Chris / Fowler, Tom

    Scientific reports

    2024  Volume 14, Issue 1, Page(s) 7475

    Abstract: To detect SARS-CoV-2 amongst asymptomatic care home staff in England, a dual-technology weekly testing regime was introduced on 23 December 2020. A lateral flow device (LFD) and quantitative reverse transcription polymerase chain reaction (qRT-PCR) test ... ...

    Abstract To detect SARS-CoV-2 amongst asymptomatic care home staff in England, a dual-technology weekly testing regime was introduced on 23 December 2020. A lateral flow device (LFD) and quantitative reverse transcription polymerase chain reaction (qRT-PCR) test were taken on the same day (day 0) and a midweek LFD test was taken three to four days later. We evaluated the effectiveness of using dual-technology to detect SARS-CoV-2 between December 2020 to April 2021. Viral concentrations derived from qRT-PCR were used to determine the probable stage of infection and likely level of infectiousness. Day 0 PCR detected 1,493 cases of COVID-19, of which 53% were in the early stages of infection with little to no risk of transmission. Day 0 LFD detected 83% of cases that were highly likely to be infectious. On average, LFD results were received 46.3 h earlier than PCR, enabling removal of likely infectious staff from the workplace quicker than by weekly PCR alone. Demonstrating the rapidity of LFDs to detect highly infectious cases could be combined with the ability of PCR to detect cases in the very early stages of infection. In practice, asymptomatic care home staff were removed from the workplace earlier, breaking potential chains of transmission.
    MeSH term(s) Humans ; SARS-CoV-2/genetics ; COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19 Testing ; England/epidemiology
    Language English
    Publishing date 2024-03-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-024-57817-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: PCR testing of traced contacts for SARS-CoV-2 in England, January to July 2021.

    Nonnenmacher, Toby / Dandamudi, Niharika / Futschik, Matthias Erwin / Tunkel, Sarah A / Kulasegaran-Shylini, Raghavendran / Germanacos, Nick / Cole-Hamilton, Joanna / Blandford, Edward / Goddard, Ashley / Hillier, Joe / Finer, Stephen / Hopkins, Susan / Fowler, Tom

    Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin

    2023  Volume 28, Issue 44

    Abstract: BackgroundThe NHS Test and Trace (NHSTT) programme was established in May 2020 in England to deliver SARS-CoV-2 testing and contact tracing in order to identify infected individuals and reduce COVID-19 spread. To further control transmission, people ... ...

    Abstract BackgroundThe NHS Test and Trace (NHSTT) programme was established in May 2020 in England to deliver SARS-CoV-2 testing and contact tracing in order to identify infected individuals and reduce COVID-19 spread. To further control transmission, people identified as contacts were asked to self-isolate for 10 days and test only if they became symptomatic. From March 2021, eligibility criteria for PCR testing expanded to include asymptomatic contacts of confirmed cases.AimTo analyse testing patterns of contacts before and after the change in testing guidance in England to assess the impact on PCR testing behaviour with respect to symptom status and contact type.MethodsTesting and contact tracing data were extracted from the national data systems and linked. Subsequently, descriptive statistical analysis was applied to identify trends in testing behaviour.ResultsBetween 1 January and 31 July 2021, over 5 million contacts were identified and reached by contact tracers; 42.3% took a PCR test around the time they were traced. Overall positivity rate was 44.3% and consistently higher in symptomatic (60-70%) than asymptomatic (around 20%, March-June) contacts. The proportion of tests taken by asymptomatic contacts increased over time, especially after the change in testing guidance. No link was observed between uptake of PCR tests and vaccination coverage. Fully vaccinated contacts showed lower positivity (23.8%) than those with one dose (37.2%) or unvaccinated (51.0%).ConclusionAlmost 1 million asymptomatic contacts were tested for SARS-CoV-2, identifying 214,056 positive cases, demonstrating the value of offering PCR testing to this group.
    MeSH term(s) Humans ; SARS-CoV-2/genetics ; COVID-19 Testing ; COVID-19/diagnosis ; COVID-19/epidemiology ; Polymerase Chain Reaction ; England/epidemiology
    Language English
    Publishing date 2023-11-02
    Publishing country Sweden
    Document type Journal Article
    ZDB-ID 1338803-4
    ISSN 1560-7917 ; 1025-496X
    ISSN (online) 1560-7917
    ISSN 1025-496X
    DOI 10.2807/1560-7917.ES.2023.28.44.2300019
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: 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.

    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 / Walker, Ann Sarah

    BMC medicine

    2024  Volume 22, Issue 1, Page(s) 143

    Abstract: Background: Syndromic surveillance often relies on patients presenting to healthcare. Community cohorts, although more challenging to recruit, could provide additional population-wide insights, particularly with SARS-CoV-2 co-circulating with other ... ...

    Abstract Background: Syndromic surveillance often relies on patients presenting to healthcare. Community cohorts, although more challenging to recruit, could provide additional population-wide insights, particularly with SARS-CoV-2 co-circulating with other respiratory viruses.
    Methods: We estimated the positivity and incidence of SARS-CoV-2, influenza A/B, and RSV, and trends in self-reported symptoms including influenza-like illness (ILI), over the 2022/23 winter season in a broadly representative UK community cohort (COVID-19 Infection Survey), using negative-binomial generalised additive models. We estimated associations between test positivity and each of the symptoms and influenza vaccination, using adjusted logistic and multinomial models.
    Results: Swabs taken at 32,937/1,352,979 (2.4%) assessments tested positive for SARS-CoV-2, 181/14,939 (1.2%) for RSV and 130/14,939 (0.9%) for influenza A/B, varying by age over time. Positivity and incidence peaks were earliest for RSV, then influenza A/B, then SARS-CoV-2, and were highest for RSV in the youngest and for SARS-CoV-2 in the oldest age groups. Many test positives did not report key symptoms: middle-aged participants were generally more symptomatic than older or younger participants, but still, only ~ 25% reported ILI-WHO and ~ 60% ILI-ECDC. Most symptomatic participants did not test positive for any of the three viruses. Influenza A/B-positivity was lower in participants reporting influenza vaccination in the current and previous seasons (odds ratio = 0.55 (95% CI 0.32, 0.95)) versus neither season.
    Conclusions: Symptom profiles varied little by aetiology, making distinguishing SARS-CoV-2, influenza and RSV using symptoms challenging. Most symptoms were not explained by these viruses, indicating the importance of other pathogens in syndromic surveillance. Influenza vaccination was associated with lower rates of community influenza test positivity.
    MeSH term(s) Middle Aged ; Humans ; Influenza, Human/epidemiology ; SARS-CoV-2 ; Seasons ; Self Report ; COVID-19 ; Virus Diseases ; Respiratory Syncytial Viruses ; United Kingdom ; Respiratory Syncytial Virus Infections/epidemiology
    Language English
    Publishing date 2024-03-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 2131669-7
    ISSN 1741-7015 ; 1741-7015
    ISSN (online) 1741-7015
    ISSN 1741-7015
    DOI 10.1186/s12916-024-03351-w
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  10. Article ; Online: Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022-23.

    Cane, Jennifer / Sanderson, Nicholas / Barnett, Sophie / Vaughan, Ali / Pott, Megan / Kapel, Natalia / Morgan, Marcus / Jesuthasan, Gerald / Samuel, Reggie / Ehsaan, Muhammad / Boothe, Hugh / Haduli, Eric / Studley, Ruth / Rourke, Emma / Diamond, Ian / Fowler, Tom / Watson, Conall / Stoesser, Nicole / Walker, Ann Sarah /
    Street, Teresa / Eyre, David

    The Journal of infection

    2024  , Page(s) 106164

    Abstract: Objectives: We evaluated Nanopore sequencing for influenza surveillance.: Methods: Influenza A and B PCR-positive samples from hospital patients in Oxfordshire, UK, and a UK-wide population survey from winter 2022-23 underwent Nanopore sequencing ... ...

    Abstract Objectives: We evaluated Nanopore sequencing for influenza surveillance.
    Methods: Influenza A and B PCR-positive samples from hospital patients in Oxfordshire, UK, and a UK-wide population survey from winter 2022-23 underwent Nanopore sequencing following targeted rt-PCR amplification.
    Results: From 941 infections, successful sequencing was achieved in 292/388(75%) available Oxfordshire samples: 231(79%) A/H3N2, 53(18%) A/H1N1, and 8(3%) B/Victoria and in 53/113(47%) UK-wide samples. Sequencing was more successful at lower Ct values. Most same-sample replicate sequences had identical haemagglutinin segments (124/141;88%); 36/39(92%) Illumina vs. Nanopore comparisons were identical, and 3(8%) differed by 1 variant. Comparison of Oxfordshire and UK-wide sequences showed frequent inter-regional transmission. Infections were closely-related to 2022-23 vaccine strains. Only one sample had a neuraminidase inhibitor resistance mutation. 849/941(90%) Oxfordshire infections were community-acquired. 63/88(72%) potentially healthcare-associated cases shared a hospital ward with ≥1 known infectious case. 33 epidemiologically-plausible transmission links had sequencing data for both source and recipient: 8 were within ≤5 SNPs, of these, 5(63%) involved potential sources that were also hospital-acquired.
    Conclusions: Nanopore influenza sequencing was reproducible and antiviral resistance rare. Inter-regional transmission was common; most infections were genomically similar. Hospital-acquired infections are likely an important source of nosocomial transmission and should be prioritised for infection prevention and control.
    Language English
    Publishing date 2024-04-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 424417-5
    ISSN 1532-2742 ; 0163-4453
    ISSN (online) 1532-2742
    ISSN 0163-4453
    DOI 10.1016/j.jinf.2024.106164
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