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  1. Article: Point of care SARS-CoV-2 nucleic acid testing in schools improves school attendance.

    Collier, Dami A / Bousfield, Rachel / Gkrania-Klotsas, Effrossyni / Gupta, Ravindra K

    Wellcome open research

    2022  Volume 7, Page(s) 8

    Abstract: Background: ...

    Abstract Background:
    Language English
    Publishing date 2022-09-06
    Publishing country England
    Document type Journal Article
    ISSN 2398-502X
    ISSN 2398-502X
    DOI 10.12688/wellcomeopenres.17213.2
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  2. Article: Traveller's molluscum.

    Collier, Dami / Wiley, Emma / Ward, Andrew / Hedley, Lucy

    British journal of hospital medicine (London, England : 2005)

    2014  Volume 75, Issue 10, Page(s) 590–591

    MeSH term(s) Adult ; Amphotericin B/administration & dosage ; Antifungal Agents/administration & dosage ; Asia, Southeastern/epidemiology ; Bone Marrow Examination/methods ; CD4 Lymphocyte Count ; Diagnosis, Differential ; Drug Administration Routes ; Female ; HIV ; HIV Infections/complications ; HIV Infections/immunology ; Humans ; Itraconazole/administration & dosage ; Mycoses/drug therapy ; Mycoses/etiology ; Mycoses/microbiology ; Mycoses/physiopathology ; Penicillium/drug effects ; Penicillium/isolation & purification ; Travel ; Treatment Outcome ; Viral Load
    Chemical Substances Antifungal Agents ; liposomal amphotericin B ; Itraconazole (304NUG5GF4) ; Amphotericin B (7XU7A7DROE)
    Language English
    Publishing date 2014-10
    Publishing country England
    Document type Case Reports ; Journal Article
    ISSN 1750-8460
    ISSN 1750-8460
    DOI 10.12968/hmed.2014.75.10.590
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Active and passive case-finding in tuberculosis-affected households in Peru: a 10-year prospective cohort study.

    Saunders, Matthew J / Tovar, Marco A / Collier, Dami / Baldwin, Matthew R / Montoya, Rosario / Valencia, Teresa R / Gilman, Robert H / Evans, Carlton A

    The Lancet. Infectious diseases

    2019  Volume 19, Issue 5, Page(s) 519–528

    Abstract: Background: Active case-finding among contacts of patients with tuberculosis is a global health priority, but the effects of active versus passive case-finding are poorly characterised. We assessed the contribution of active versus passive case-finding ... ...

    Abstract Background: Active case-finding among contacts of patients with tuberculosis is a global health priority, but the effects of active versus passive case-finding are poorly characterised. We assessed the contribution of active versus passive case-finding to tuberculosis detection among contacts and compared sex and disease characteristics between contacts diagnosed through these strategies.
    Methods: In shanty towns in Callao, Peru, we identified index patients with tuberculosis and followed up contacts aged 15 years or older for tuberculosis. All patients and contacts were offered free programmatic active case-finding entailing sputum smear microscopy and clinical assessment. Additionally, all contacts were offered intensified active case-finding with sputum smear and culture testing monthly for 6 months and then once every 4 years. Passive case-finding at local health facilities was ongoing throughout follow-up.
    Findings: Between Oct 23, 2002, and May 26, 2006, we identified 2666 contacts, who were followed up until March 1, 2016. Median follow-up was 10·0 years (IQR 7·5-11·0). 232 (9%) of 2666 contacts were diagnosed with tuberculosis. The 2-year cumulative risk of tuberculosis was 4·6% (95% CI 3·5-5·5), and overall incidence was 0·98 cases (95% CI 0·86-1·10) per 100 person-years. 53 (23%) of 232 contacts with tuberculosis were diagnosed through active case-finding and 179 (77%) were identified through passive case-finding. During the first 6 months of the study, 23 (45%) of 51 contacts were diagnosed through active case-finding and 28 (55%) were identified through passive case-finding. Contacts diagnosed through active versus passive case-finding were more frequently female (36 [68%] of 53 vs 85 [47%] of 179; p=0·009), had a symptom duration of less than 15 days (nine [25%] of 36 vs ten [8%] of 127; p=0·03), and were more likely to be sputum smear-negative (33 [62%] of 53 vs 62 [35%] of 179; p=0·0003).
    Interpretation: Although active case-finding made an important contribution to tuberculosis detection among contacts, passive case-finding detected most of the tuberculosis burden. Compared with passive case-finding, active case-finding was equitable, helped to diagnose tuberculosis earlier and usually before a positive result on sputum smear microscopy, and showed a high burden of undetected tuberculosis among women.
    Funding: Wellcome Trust, Department for International Development Civil Society Challenge Fund, Joint Global Health Trials consortium, Bill & Melinda Gates Foundation, Imperial College National Institutes of Health Research Biomedical Research Centre, Foundation for Innovative New Diagnostics, Sir Halley Stewart Trust, WHO, TB REACH, and IFHAD: Innovation for Health and Development.
    MeSH term(s) Adult ; Contact Tracing/statistics & numerical data ; Family Characteristics ; Female ; Follow-Up Studies ; Humans ; Incidence ; Male ; Peru/epidemiology ; Prospective Studies ; Sex Factors ; Sputum/microbiology ; Tuberculosis/diagnosis ; Tuberculosis/epidemiology ; Tuberculosis/prevention & control ; Young Adult
    Language English
    Publishing date 2019-03-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2061641-7
    ISSN 1474-4457 ; 1473-3099
    ISSN (online) 1474-4457
    ISSN 1473-3099
    DOI 10.1016/S1473-3099(18)30753-9
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  4. Article ; Online: Recurrent emergence and transmission of a SARS-CoV-2 Spike deletion ΔH69/V70

    Kemp, Steven / Datir, Rawlings / Collier, Dami / Ferreira, Isabella / Carabelii, Alessandro / Harvey, William / Robertson, David L / Gupta, Ravindra K

    bioRxiv

    Abstract: SARS-CoV-2 Spike amino acid mutations in the receptor binding domain (RBD) are becoming more common and thought to arise from immune selection pressure. Deletions in the N terminal domain are also being described, though their role is unclear. Here we ... ...

    Abstract SARS-CoV-2 Spike amino acid mutations in the receptor binding domain (RBD) are becoming more common and thought to arise from immune selection pressure. Deletions in the N terminal domain are also being described, though their role is unclear. Here we report recurrent, independent acquisitions and transmissions of the Spike double deletion ΔH69/ΔV70 following receptor binding mutations such as N501Y, N439K and Y453F. In addition we report a sub-lineage of over 350 sequences bearing seven spike mutations across the RBD (N501Y, A570D), S1 (ΔH69/ΔV70) and S2 (P681H, T716I, S982A and D1118H) in England. We present data that ΔH69/ΔV70 increases Spike-mediated infectivity by approximately two fold and therefore may be a compensatory mechanism for putative antibody escape mutations in Spike. Enhanced surveillance for this deletion with and without RBD mutations should be considered as a priority.
    Keywords covid19
    Language English
    Publishing date 2020-12-15
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2020.12.14.422555
    Database COVID19

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  5. Article: Feasibility and cost analysis of programmatic implementation of Microscopic-Observation Drug Susceptibility (MODS) assay in Nigeria.

    Ochang, Ernest Afu / Oduyebo, Oyinlola O / Onwuezobe, Ifeanyi A / Collier, Dami / Bode-Sojobi, Ibidunni / Odo, Michael

    Nigerian journal of medicine : journal of the National Association of Resident Doctors of Nigeria

    2018  Volume 25, Issue 3, Page(s) 226–233

    Abstract: Objectives: Detection of Multi-drug resistant tuberculosis in Nigeria still remains a challenge. We evaluated the feasibility of programmatic implementation of the Microscopic-Observation Drug Susceptibility (MODS) assay, a rapid culture and drug ... ...

    Abstract Objectives: Detection of Multi-drug resistant tuberculosis in Nigeria still remains a challenge. We evaluated the feasibility of programmatic implementation of the Microscopic-Observation Drug Susceptibility (MODS) assay, a rapid culture and drug susceptibility testing technique for drug susceptibility testing in a low resource setting.
    Method: In a novel laboratory setting in Nigeria, we obtained data from the market on the cost of materials necessary for MODS assay. Three routinely collected sputum specimens from 160 tuberculosis suspects were evaluated by smear microscopy while only the early morning specimen was used for MODS culture.
    Results: MODS assay detected M. tuberculosis in 97.7% (42/43) of smear positive and 6.0% (7/117) of smear negative TB suspects. There was a statistically significant advantage of a single MODS culture over 3 smear microscopies (P=0.019). The modal time from culture of specimen to detection of M. tuberculosis and availability of drug susceptibility result for MODS was 7days with a mean of 8.4 days (Range= 5-13 days). Culture and susceptibility result was available in 18.4% (9/49) of patients within 5days of culture. Turnaround time for smear microscopy in the centers was 3 days. Cost of processing one specimen by MODS assay in the study was USD2.65. Multi-Drug resistant tuberculosis (MDR-TB) was detected in 4.1% (2/49) while Isoniazid mono-resistance was detected in 2.0% (1/49) of the culture positive cases. All the drug resistant isolates were from re-treatment cases with a statistically significant association (P=0.005).
    Conclusion: The MODS technique is simple, and its implementation in this novel setting was feasible. MODS can be scaled up to meet the demand for MDR-TB confirmation in XpertMTB/Rif deployed sites in Nigeria.
    MeSH term(s) Adult ; Antitubercular Agents/therapeutic use ; Costs and Cost Analysis ; Culture Techniques ; Feasibility Studies ; Female ; Humans ; Isoniazid/therapeutic use ; Male ; Microbial Sensitivity Tests/economics ; Microscopy/economics ; Middle Aged ; Mycobacterium tuberculosis/isolation & purification ; Mycobacterium tuberculosis/physiology ; Nigeria ; Program Evaluation ; Sputum/microbiology ; Tuberculosis, Multidrug-Resistant/diagnosis ; Tuberculosis, Multidrug-Resistant/drug therapy ; Tuberculosis, Multidrug-Resistant/microbiology ; Tuberculosis, Multidrug-Resistant/pathology ; Young Adult
    Chemical Substances Antitubercular Agents ; Isoniazid (V83O1VOZ8L)
    Language English
    Publishing date 2018-07-16
    Publishing country Nigeria
    Document type Journal Article
    ISSN 1115-2613
    ISSN 1115-2613
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Atypical B cells and impaired SARS-CoV-2 neutralization following heterologous vaccination in the elderly.

    Ferreira, Isabella A T M / Lee, Colin Y C / Foster, William S / Abdullahi, Adam / Dratva, Lisa M / Tuong, Zewen Kelvin / Stewart, Benjamin J / Ferdinand, John R / Guillaume, Stephane M / Potts, Martin O P / Perera, Marianne / Krishna, Benjamin A / Peñalver, Ana / Cabantous, Mia / Kemp, Steven A / Ceron-Gutierrez, Lourdes / Ebrahimi, Soraya / Lyons, Paul / Smith, Kenneth G C /
    Bradley, John / Collier, Dami A / McCoy, Laura E / van der Klaauw, Agatha / Thaventhiran, James E D / Farooqi, I Sadaf / Teichmann, Sarah A / MacAry, Paul A / Doffinger, Rainer / Wills, Mark R / Linterman, Michelle A / Clatworthy, Menna R / Gupta, Ravindra K

    Cell reports

    2023  Volume 42, Issue 8, Page(s) 112991

    Abstract: Suboptimal responses to a primary vaccination course have been reported in the elderly, but there is little information regarding the impact of age on responses to booster third doses. Here, we show that individuals 70 years or older (median age 73, ... ...

    Abstract Suboptimal responses to a primary vaccination course have been reported in the elderly, but there is little information regarding the impact of age on responses to booster third doses. Here, we show that individuals 70 years or older (median age 73, range 70-75) who received a primary two-dose schedule with AZD1222 and booster third dose with mRNA vaccine achieve significantly lower neutralizing antibody responses against SARS-CoV-2 spike pseudotyped virus compared with those younger than 70 (median age 66, range 54-69) at 1 month post booster. Impaired neutralization potency and breadth post third dose in the elderly is associated with circulating "atypical" spike-specific B cells expressing CD11c and FCRL5. However, when considering individuals who received three doses of mRNA vaccine, we did not observe differences in neutralization or enrichment in atypical B cells. This work highlights the finding that AdV and mRNA COVID-19 vaccine formats differentially instruct the memory B cell response.
    MeSH term(s) Aged ; Humans ; COVID-19/prevention & control ; COVID-19 Vaccines ; ChAdOx1 nCoV-19 ; SARS-CoV-2 ; Vaccination
    Chemical Substances COVID-19 Vaccines ; ChAdOx1 nCoV-19 (B5S3K2V0G8)
    Language English
    Publishing date 2023-08-16
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2023.112991
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Virological Outcomes of Second-line Protease Inhibitor-Based Treatment for Human Immunodeficiency Virus Type 1 in a High-Prevalence Rural South African Setting: A Competing-Risks Prospective Cohort Analysis.

    Collier, Dami / Iwuji, Collins / Derache, Anne / de Oliveira, Tulio / Okesola, Nonhlanhla / Calmy, Alexandra / Dabis, Francois / Pillay, Deenan / Gupta, Ravindra K

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

    2017  Volume 64, Issue 8, Page(s) 1006–1016

    Abstract: Background: Second-line antiretroviral therapy (ART) based on ritonavir-boosted protease inhibitors (bPIs) represents the only available option after first-line failure for the majority of individuals living with human immunodeficiency virus (HIV) ... ...

    Abstract Background: Second-line antiretroviral therapy (ART) based on ritonavir-boosted protease inhibitors (bPIs) represents the only available option after first-line failure for the majority of individuals living with human immunodeficiency virus (HIV) worldwide. Maximizing their effectiveness is imperative.
    Methods: This cohort study was nested within the French National Agency for AIDS and Viral Hepatitis Research (ANRS) 12249 Treatment as Prevention (TasP) cluster-randomized trial in rural KwaZulu-Natal, South Africa. We prospectively investigated risk factors for virological failure (VF) of bPI-based ART in the combined study arms. VF was defined by a plasma viral load >1000 copies/mL ≥6 months after initiating bPI-based ART. Cumulative incidence of VF was estimated and competing risk regression was used to derive the subdistribution hazard ratio (SHR) of the associations between VF and patient clinical and demographic factors, taking into account death and loss to follow-up.
    Results: One hundred one participants contributed 178.7 person-years of follow-up. Sixty-five percent were female; the median age was 37.4 years. Second-line ART regimens were based on ritonavir-boosted lopinavir, combined with zidovudine or tenofovir plus lamivudine or emtricitabine. The incidence of VF on second-line ART was 12.9 per 100 person-years (n = 23), and prevalence of VF at censoring was 17.8%. Thirteen of these 23 (56.5%) virologic failures resuppressed after a median of 8.0 months (interquartile range, 2.8-16.8 months) in this setting where viral load monitoring was available. Tuberculosis treatment was associated with VF (SHR, 11.50 [95% confidence interval, 3.92-33.74]; P < .001).
    Conclusions: Second-line VF was frequent in this setting. Resuppression occurred in more than half of failures, highlighting the value of viral load monitoring of second-line ART. Tuberculosis was associated with VF; therefore, novel approaches to optimize the effectiveness of PI-based ART in high-tuberculosis-burden settings are needed.
    Clinical trials registration: NCT01509508.
    MeSH term(s) Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anti-HIV Agents/therapeutic use ; Female ; Genotype ; HIV Infections/complications ; HIV Infections/drug therapy ; HIV Infections/epidemiology ; HIV Infections/virology ; HIV Protease Inhibitors/therapeutic use ; HIV-1/classification ; HIV-1/genetics ; HIV-1/isolation & purification ; Humans ; Male ; Middle Aged ; Prevalence ; Prospective Studies ; Rural Population ; South Africa/epidemiology ; Treatment Outcome ; Tuberculosis/complications ; Viral Load ; Young Adult
    Chemical Substances Anti-HIV Agents ; HIV Protease Inhibitors
    Language English
    Publishing date 2017-03-22
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1099781-7
    ISSN 1537-6591 ; 1058-4838
    ISSN (online) 1537-6591
    ISSN 1058-4838
    DOI 10.1093/cid/cix015
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  8. Article ; Online: Diffuse White Matter Signal Abnormalities on Magnetic Resonance Imaging Are Associated With Human Immunodeficiency Virus Type 1 Viral Escape in the Central Nervous System Among Patients With Neurological Symptoms.

    Kugathasan, Ruthiran / Collier, Dami A / Haddow, Lewis J / El Bouzidi, Kate / Edwards, Simon G / Cartledge, Jonathan D / Miller, Robert F / Gupta, Ravindra K

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

    2017  Volume 64, Issue 8, Page(s) 1059–1065

    Abstract: Background: Human immunodeficiency virus type 1 (HIV-1) can replicate independently in extravascular compartments such as the central nervous system, resulting in either cerebrospinal fluid (CSF) discordance (viral load [VL] in CSF 0.5 log10 copies HIV- ... ...

    Abstract Background: Human immunodeficiency virus type 1 (HIV-1) can replicate independently in extravascular compartments such as the central nervous system, resulting in either cerebrospinal fluid (CSF) discordance (viral load [VL] in CSF 0.5 log10 copies HIV-1 RNA greater than plasma VL) or escape (detection of HIV VL >50 copies/mL in CSF in patients with suppressed plasma VL <50 copies/mL). Both discordance and escape may be associated with neurological symptoms. We explored risk factors for CSF discordance and escape in patients presenting with diverse neurological problems.
    Methods: HIV-infected adult patients undergoing diagnostic lumbar puncture (LP) at a single center between 2011 and 2015 were included in the analysis. Clinical and neuroimaging variables associated with CSF discordance/escape were identified using multivariate logistic regression.
    Results: One hundred forty-six patients with a median age of 45.3 (interquartile range [IQR], 39.6-51.5) years underwent 163 LPs. Median CD4 count was 430 (IQR, 190-620) cells/µL. Twenty-four (14.7%) LPs in 22 patients showed CSF discordance, of which 10 (6.1%) LPs in 9 patients represented CSF escape. In multivariate analysis, both CSF discordance and escape were associated with diffuse white matter signal abnormalities (DWMSAs) on cranial magnetic resonance imaging (adjusted odds ratio, 10.3 [95% confidence interval {CI}, 2.3-45.0], P = .007 and 56.9 [95% CI, 4.0-882.8], P = .01, respectively). All 7 patients with CSF escape (10 LPs) had been diagnosed with HIV >7 years prior to LP, and 6 of 6 patients with resistance data had documented evidence of drug-resistant virus in plasma.
    Conclusions: Among patients presenting with diverse neurological problems, CSF discordance or escape was observed in 15%, with treatment-experienced patients dominating the escape group. DWMSAs in HIV-infected individuals presenting with neurological problems should raise suspicion of possible CSF discordance/escape.
    MeSH term(s) AIDS Dementia Complex/pathology ; AIDS Dementia Complex/virology ; Adult ; Aged ; Aged, 80 and over ; Cerebrospinal Fluid/virology ; Female ; HIV Infections/complications ; HIV Infections/virology ; HIV-1/isolation & purification ; Humans ; Magnetic Resonance Imaging ; Male ; Middle Aged ; Retrospective Studies ; Viral Load ; White Matter/diagnostic imaging ; White Matter/pathology ; Young Adult
    Language English
    Publishing date 2017--15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1099781-7
    ISSN 1537-6591 ; 1058-4838
    ISSN (online) 1537-6591
    ISSN 1058-4838
    DOI 10.1093/cid/cix035
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  9. Article ; Online: Author Correction: SARS-CoV-2 evolution during treatment of chronic infection.

    Kemp, Steven A / Collier, Dami A / Datir, Rawlings P / Ferreira, Isabella A T M / Gayed, Salma / Jahun, Aminu / Hosmillo, Myra / Rees-Spear, Chloe / Mlcochova, Petra / Lumb, Ines Ushiro / Roberts, David J / Chandra, Anita / Temperton, Nigel / Sharrocks, Katherine / Blane, Elizabeth / Modis, Yorgo / Leigh, Kendra E / Briggs, John A G / van Gils, Marit J /
    Smith, Kenneth G C / Bradley, John R / Smith, Chris / Doffinger, Rainer / Ceron-Gutierrez, Lourdes / Barcenas-Morales, Gabriela / Pollock, David D / Goldstein, Richard A / Smielewska, Anna / Skittrall, Jordan P / Gouliouris, Theodore / Goodfellow, Ian G / Gkrania-Klotsas, Effrossyni / Illingworth, Christopher J R / McCoy, Laura E / Gupta, Ravindra K

    Nature

    2022  Volume 608, Issue 7922, Page(s) E23

    Language English
    Publishing date 2022-07-21
    Publishing country England
    Document type Published Erratum
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-022-05104-2
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  10. Article ; Online: Author Correction: Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies.

    Collier, Dami A / De Marco, Anna / Ferreira, Isabella A T M / Meng, Bo / Datir, Rawlings P / Walls, Alexandra C / Kemp, Steven A / Bassi, Jessica / Pinto, Dora / Silacci-Fregni, Chiara / Bianchi, Siro / Tortorici, M Alejandra / Bowen, John / Culap, Katja / Jaconi, Stefano / Cameroni, Elisabetta / Snell, Gyorgy / Pizzuto, Matteo S / Pellanda, Alessandra Franzetti /
    Garzoni, Christian / Riva, Agostino / Elmer, Anne / Kingston, Nathalie / Graves, Barbara / McCoy, Laura E / Smith, Kenneth G C / Bradley, John R / Temperton, Nigel / Ceron-Gutierrez, Lourdes / Barcenas-Morales, Gabriela / Harvey, William / Virgin, Herbert W / Lanzavecchia, Antonio / Piccoli, Luca / Doffinger, Rainer / Wills, Mark / Veesler, David / Corti, Davide / Gupta, Ravindra K

    Nature

    2022  Volume 608, Issue 7922, Page(s) E24

    Language English
    Publishing date 2022-07-22
    Publishing country England
    Document type Published Erratum
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-022-05103-3
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