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1. The prevalence of sleep disorders in Iranian adults - an epidemiological study

Author

Khazaie, Habibolah, Jalali, Amir, Khazaie, Amirhossein, Mohammadi, Reza, Jalali, Romina, Moheb, Sobhan Bagheri, Ghalebandi, Mirfarhad, Kashaninasab, Fatemeh, Ghaleiha, Ali, Shalbafan, Mohammadreza, Ardekani, Seyed Mojtaba Yassini, Maroufi, Azad, Ezzati, Ebrahim, Dastgheib, Seyed Ali, Bordbar, Mohammadreza Fayyazi, Khoozan, Mahboobeh, Negahban, Saeedeh, Ghoreishi, Seyed Abolfazl, Rezaei, Farzin, Saki, Koresh, Jalali, Ali, Salimi, Yahya, and Ardakan, Mohammad Raza Khodaie

Published
2024
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6. A child with sickle cell disease admitted with coronavirus disease 2019 pneumonia and acute chest syndrome in pediatric intensive care unit: A case report

Author

Mohammad Raza, Saleh Saad Alshehri, and Mohsina Reshma Pasha

Subjects
Medicine (General), R5-920
Abstract

Management of sickle cell disease complications in the setting of the coronavirus disease 2019 (COVID-19) pandemic is complicated with little published pediatric data. We report the first documented case of a 9-year-old boy with sickle cell disease, presenting with fever, cough, and shortness of breath, diagnosed to have acute chest syndrome and coronavirus disease 2019 (COVID-19) pneumonia with inflammatory storm requiring ventilation, exchange blood transfusion, immunomodulatory agents, and prophylactic anticoagulation. The patient responded satisfactorily to the management of the acute illness and was found to be well at the next visit to the pediatric hematology outpatient department following hospital discharge.

Published
2024
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7. Large-Size ultrathin mica nanosheets: Reinforcements of biobased PEF polyester

Author

Jiheng Ding, Hao Wang, Hongran Zhao, Shuo Shi, Jing Su, Qinchao Chu, Bin Fang, Mohammad Raza Miah, Jinggang Wang, and Jin Zhu

Subjects
Natural mica nanosheets, Scalable exfoliation, Ultrahigh-aspect-ratio, Biobased polyester nanocomposite, High barrier and mechanical properties, Science (General), Q1-390
Abstract

Due to the superior physical properties and high-level alignment of the nanoscale building blocks, assembly of high-quality two-dimensional (2D) nanosheets into macroscopic engineering structure materials can achieve many unexpected performance. Natural mica nanosheets (MNSs) are abundant and with superlative properties, showing huge prospect for engineering structural materials. However, the difficulty of the mass production with large size and high aspect ratio are the current factors that limit this. Inspired by the well-known scotch-tape exfoliation, herein we develop a gummy-tape exfoliation (GTE) method by using liquid oligomers as mediums in ball-milling process to massively produce large-size and ultrathin MNSs. As a confirmation, the obtained MNSs show a record high aspect ratio of ≈1320 and a large actual yield of ∼ 80 %. A transparent biobased aromatic polyester nanocomposite film made of such MNSs and polyethylene furandicarboxylate (PEF) matrix possesses remarkably improved mechanical, barrier properties, and UV-shielding performances at an extremely low filler loading (≤0.5 vol%), making it a novel potential engineering material for packing fields in foods, drugs, and electronic products, etc.

Published
2024
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8. Evaluation of combined carbon dots and ciprofloxacin on the expression level of pslA, pelA, and ppyR genes and biofilm production in ciprofloxacin-resistant Pseudomonas aeruginosa isolates from burn wound infection in Iran

Author

Hamid Pajavand, Ashraf Mohabti Mobarez, Ali Barati, Maryam Nikkhah, Mohammad Raza Delnavazi, Ramin Abiri, Amir houshang Alvandi, and Rahleh Karimiravesh

Subjects
Resistant, P. aeruginosa, Carbon dot, Shikonin, Biofilm, Ciprofloxacin, Microbiology, QR1-502
Abstract

ABSTRACT: Objectives: Antimicrobial resistance and biofilm formation are increasingly significant public health concerns. This study aimed to examine the antibacterial and antibiofilm properties of carbon dots (C-dots) alone and in combination with antibiotics against biofilm-forming isolates of Pseudomonas aeruginosa. Methods: The antibacterial property of C-dots was investigated by broth microdilution method against ATCC PAO1 and P. aeruginosa clinical isolates. The antibacterial effect of the C-dots and ciprofloxacin combination was investigated using the checkerboard method. The antibiofilm effect of the C-dots alone and its combination with ciprofloxacin was evaluated using the microtiter plate method. Subsequently, the toxicity of each agent was tested on L929 fibroblast cells. In the end, the effects of C-dots on the expression levels of pslA, pelA, and ppyR genes were determined using real-time quantitative PCR. Results: The combination of C-dots and ciprofloxacin exhibited a synergistic effect. Additionally, this compound substantially decreased bacterial growth (P < 0.0001) and inhibited biofilm formation at MIC (96 µg/mL) and sub-MIC (48 µg/mL) concentrations (P < 0.0053, P < 0.01). After being exposed to C-dots at a concentration of 1mg/mL for 24 hours, the survival rate of L929 cells was 87.3%. The expression of genes pslA, pelA, and ppyR, associated with biofilm formation in P. aeruginosa, was significantly reduced upon exposure to C-dots (P < 0.0023). Conclusions: The findings demonstrate a promising new treatment method for infections. Furthermore, reducing the dosage of antibiotics can lead to an improvement in the toxic effects caused by dose-dependent antibiotics and antimicrobial activity.

Published
2023
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12. The effect of a high-intensity interval training with Portulaca oleracea supplementation on Irisin and TLR4 in the liver tissue of rats with non-alcoholic fatty liver disease

Author

Majid Farah Nia, Mohammad Raza Hosseinabadi, Mehdi Zarei, and Mahmood Soltani

Subjects
high-intensity interval training, portulaca oleracea, non-alcoholic fatty liver disease, irisin, tlr4, Medicine
Abstract

Background: Lifestyle modification through dietary interventions and exercise training is still one of the most effective ways to treat non-alcoholic fatty liver disease. The aim of this study was to investigate the effect of a high-intensity interval training along with Portulaca oleracea supplementation on Irisin and TLR4 in the liver tissues of rats with non-alcoholic fatty liver disease. Materials and Methods: In this experimental study, 30 male Wistar rats were divided into two groups: non-alcoholic fatty liver disease (n=25) and healthy control (n=5). Non-alcoholic fatty liver was induced by 12 weeks of high-fat diet. After confirming non-alcoholic fatty liver disease, rats (n=20) were assigned into four subgroups; non-alcoholic fatty liver control group (n=5), Portulaca oleracea supplement group (n=5), training group (n=5) and training group + Portulaca oleracea supplement (n=5). Portulaca oleracea supplement was given daily and a high-intensity interval training was presented for 8 weeks, 5 sessions per week. The amounts of Irisin and TLR4 in liver tissue were measured using the sandwich ELISA method. Results: Irisin levels were significantly higher in the training+Portulaca oleracea supplement group compared to the fatty liver control group (P=0.001), the interval training group (P=0.018) and Portulaca oleracea supplement group (P=0.033). The TLR4 levels in the training+Portulaca oleracea supplement group (P=0.007) and the high intensity interval training group (P=0.045) were significantly lower than the fatty liver control group. Conclusion: High-intensity interval training along with Portulaca oleracea supplementation leads to increases in Irisin release and decreases in the TLR4 levels in the liver tissue of rats with non-alcoholic fatty liver disease, which may be effective in improving non-alcoholic fatty liver disease.

Published
2023

13. Diagnostic dilemmas and challenges in the management of myasthenia in infants and toddlers: A case report

Author

Khairunnisa Mukhtiar, Mohammad Raza, Isbaah Tejani, Farhan Ali, and Shahnaz Ibrahim

Subjects
Medicine (General), R5-920
Abstract

Myasthenia in the infancy and toddler age group is rare and often presents a challenge to treating pediatric neurologists. Our report addresses the challenges encountered when distinguishing myasthenia in infants and toddlers from similar illnesses, as well as the differentiation between congenital myasthenia, transient myasthenia, and autoimmune myasthenia. We present four cases of myasthenia between the ages of 10 and 30 months. The diagnosis and management of these cases were challenging due to the variability in clinical presentation. Four cases of myasthenia were diagnosed, with three having autoimmune myasthenia and one having congenital myasthenic syndrome. One patient initially tested negative for acetylcholine receptor antibodies, but later tested positive after 4 months and had a rare facial diplegia finding. The patient with congenital myasthenic syndrome had a novel genetic mutation, DPAGT1 homozygous variants, and also had false positive acetylcholine receptor antibodies. These cases highlight the importance of genetic testing for all infants and toddlers suspected of having myasthenia.

Published
2023
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17. Comparison of the Effects of Mode Deactivation Therapy and Emotion Regulation on the Negative Self-Concept in Teenagers with Emotional Dysregulation

Author

Rashin Rajaei, Mahdi Zare Bahramabadi, and Mohammad Raza Abedi

Subjects
emotional dysregulation, emotion regulation, mode deactivation therapy, self-concept, Psychology, BF1-990
Abstract

One of the most important issues that teenagers face is the problems related to the dysregulation of emotions and its effect on people's self-concept. In this research, the effectiveness of mode deactivation therapy and emotion regulation on the negative self-concept of teenagers with emotion dysregulation was compared. 30 teenagers referring to the clinics of Isfahan city were selected through interviews and obtaining a high score (90) in the emotion regulation difficulty questionnaire and placed in three groups (10people), of mode deactivation therapy, emotion regulation, and control. The intervention groups received 8 sessions of 90 minutes in a period of 8 weeks, and the control group did not receive intervention. Before and after the intervention, all people answered the Rogers self-concept questionnaire. The obtained data were tested using univariate covariance analysis. The findings of the research showed that the emotion regulation therapy was able to reduce the negative self-concept of teenagers, while mode deativation therapy was not effective. The results of the research showed that emotion regulation intervention is more effective than mode deactivation in reducing the negative self-concept of teenagers

Published
2023
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23. Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7/Alpha variant infections

Author

Matthew D. Parker, Hazel Stewart, Ola M. Shehata, Benjamin B. Lindsey, Dhruv R. Shah, Sharon Hsu, Alexander J. Keeley, David G. Partridge, Shay Leary, Alison Cope, Amy State, Katie Johnson, Nasar Ali, Rasha Raghei, Joe Heffer, Nikki Smith, Peijun Zhang, Marta Gallis, Stavroula F. Louka, Hailey R. Hornsby, Hatoon Alamri, Max Whiteley, Benjamin H. Foulkes, Stella Christou, Paige Wolverson, Manoj Pohare, Samantha E. Hansford, Luke R. Green, Cariad Evans, Mohammad Raza, Dennis Wang, Andrew E. Firth, James R. Edgar, Silvana Gaudieri, Simon Mallal, The COVID-19 Genomics UK (COG-UK) consortium, Mark O. Collins, Andrew A. Peden, and Thushan I. de Silva

Subjects
Biology (General), QH301-705.5
Abstract

Matthew Parker et al. use the ARTIC network tiled amplicon PCR and Oxford Nanopore sequencing of thousands of SARS-CoV-2 samples to detect subgenomic RNA changes in the B.1.1.7 lineage endemic in the UK in late 2020/early 2021. They discovered higher subgenomic RNA in B.1.1.7 compared to previous lineages, and find a noncanonical subgenomic RNA that could encode ORF9b.

Published
2022
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24. Impact of the COVID-19 Outbreak on Air Pollutants, in 2020 Compared to the Same Period in 2019 in Qom, Iran

Author

Zahra Safari, Reza Fouladi-Fard, Mohammad Raza Hosseini, Razieh Vahidmoghadam, Margherita Ferrante, Mostafa Rezaali, Alireza Omidi Oskouei, and Maria Fiore

Subjects
covid-19, air pollution, quarantine, qom city., Environmental technology. Sanitary engineering, TD1-1066, Environmental sciences, GE1-350
Abstract

Introduction: The present study aimed to investigate the change of air pollutants in 2020 in Qom compared to the same period in 2019 in five scenarios. Materials and Methods: The hourly air quality data was obtained from air quality monitoring stations of Qom Environmental Protection Organization (EPO). The meteorological parameters were obtained from Iranian Meteorological Organization website. The data were analyzed using Excel, SPSS, and WRPLOT view. Results: In the first month of the COVID-19 crisis, NO2, SO2, and CO decreased by 26.4, 39, and 0.2 µg/m3 compared to same period in 2019, respectively; however, PM2.5 and O3 increased by 7.1 and 2.3 µg/m3, respectively. In Iranian Nowruz holidays, an increase of 2.9 µg/m3 in O3 mean concentration and a decrease of 8.1, 23.8, 22.8, and 0.2 µg/m3 in mean concentration of PM10, NO2, SO2, and CO were experienced. The prevailing wind direction during the 2020 in each scenario was from the west of Qom city. Conclusion: Gaseous pollutants decreased during the crisis, but particulate pollutants increased slightly compared to the same period in 2019. The lockdown may have had the most impact in decreasing pollutants. A slight increase in wind speed from the west could be a factor in increasing particles. This crisis provided an opportunity to assess the role of policies, such as traffic reduction plans or discarding worn-out cars or urban management to improve air quality.

Published
2022

26. Characterising within-hospitalSARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves

Author

Benjamin B. Lindsey, Ch. Julián Villabona-Arenas, Finlay Campbell, Alexander J. Keeley, Matthew D. Parker, Dhruv R. Shah, Helena Parsons, Peijun Zhang, Nishchay Kakkar, Marta Gallis, Benjamin H. Foulkes, Paige Wolverson, Stavroula F. Louka, Stella Christou, Amy State, Katie Johnson, Mohammad Raza, Sharon Hsu, Thibaut Jombart, Anne Cori, Sheffield COVID-19 Genomics Group, The COVID-19 Genomics UK (COG-UK) consortium, CMMID COVID-19 working group, Cariad M. Evans, David G. Partridge, Katherine E. Atkins, Stéphane Hué, and Thushan I. de Silva

Subjects
Science
Abstract

SARS-CoV-2 has resulted in multiple outbreaks in hospitals, but identifying transmission events is challenging. Here, the authors combine whole genome sequencing and epidemiological data from the first two waves of the pandemic at a UK hospital trust and characterise transmission chains.

Published
2022
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31. The Role of Sex, Perceived Pain, and Illness Perceptions in Disease Activity in Rheumatoid Arthritis

Author

Mohammad Raza Seirafi, Sarah Namjoo, and Mehrdad Sabet

Subjects
rheumatoid arthritis, disease activity, pain, illness perception, sex differences, Medicine
Abstract

Background: In the “treating to target” strategy for Rheumatoid Arthritis (RA) management, “cognitive” beyond “physical” measures allow a more comprehensive assessment. Objective: This study reported a predictive analysis of patients on disease activity and the degree to which these predictions could be uniquely attributable to Illness Perception (IP), pain, and sex differences. Methods: This cross-sectional study was conducted on 108 patients with Rheumatoid Arthritis aged 18 to 65 years old, selected via convenience sampling. Measurements were done using Disease Activity Score in 28 Joints (DAS28), patient’s Illness Perception Questionnaire (IPQ-R), and Numerical Rating Scale (NRS) for perceived pain. Data were analyzed applying Spearman and Pearson correlation coefficients and Multiple Stepwise Regression (MSR). Results: In correlation analysis, the sex- Disease Activity association (0.40, P

Published
2021
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35. Correlation Between the Acoustic and Cell Morphology of Polyurethane/Silica Nanocomposite Foams: Effect of Various Proportions of Silica at Low Frequency Region

Author

Marziye Pirani, Mohammad Raza Monazzam, and Seyed Qasem Pourjandaghi

Subjects
polyurethane, nanoparticles, sound absorption coefficient, low frequency., Environmental pollution, TD172-193.5
Abstract

Introduction: Reducing noise pollution has become an essential issue due to the increase in public concern and also social demands for a better lifestyle. Using sound absorption materials is a preferred method to reduce the noise pollution. Undesirable properties of pure polyurethane such as poor absorption of mechanical energy in narrow frequency ranges can be improved by providing polymeric nanocomposites. The main purpose of this study is to synthesize the polyurethane nanocomposite foams in order to improve its acoustic properties. Material and Methods: At the first steage, pure polyurethane foam was synthesized using the pre-polymer method. Afterwards, nanocomposite foams were synthesized with different mass fractions of Nano silica. The cellular morphology of prepared nanocomposite foams was investigated by scanning electron microscopy (SEM (.Utilizing a two-microphone impedance tube, sound absorption coefficient (α) was calculated in the frequency ranges of 100 Hz to 1600 Hz in order to investigate the acoustic properties of the new absorbant. Results: According to the microscopic investigations, morphology of the cells changed after adding silica nanoparticles. Also, the cell sizes were observed to be decreased by increasing the amount of silica nanoparticles. Furthermore, the acoustic analysis of nanocomposite foams indicated that the sound absorption increased by enhancing the load of silica nanoparticles. Conclusion: In the current study, the effect of silica nanoparticles additive amount on acoustic properties of the polyurethane-based nanocomposite was investigated. Our findings depicted that the polyurethane-based nanocomposites were able to promote the sound absorption coefficient.

Published
2021

39. Teachers 'lived Experiences in Identifying Students' Talents Based on the Dimensions and Components of the Effective Teaching Pattern

Author

Mohammad Raza Nazarian, ahmad abedi, Ali Mahdad, and MOHAMMAD ALI nadi

Subjects
life experiences, effective teaching model, students 'accounting, phenomena, Education (General), L7-991
Abstract

The purpose of this study was to study teachers 'lived experiences in identifying students' talents based on the dimensions and components of effective teaching model. The research method was qualitative phenomenological. The participants of the study were all teachers of elementary schools in Isfahan province education districts in the academic year 1398-1989. Purposeful and saturated sampling method was used to select participants, which included 38 individuals. Research tool was in-depth and semi-structured interviews. The method of data analysis was reflective analysis using van Manen's (1990) six-step method. Results showed that, by analyzing the data, 5 main themes (Engaging students), Learners, Opportunity to Existence, Objective-Free Evaluation, and Development of Perceptions of Learned Content) and 15 sub-themes on the dimensions and components of an effective teaching model were identified to identify students' talents. Therefore, it is suggested that teachers use these techniques with active techniques to identify gifted students.

Published
2020
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40. Etiologic factors of Candida vulvovaginitis in pregnant women

Author

Sousan Mohammadi, Fatemeh Keshavarzi, Behnaz Manouchehri, Fariba Lahoorpour, and Mohammad Raza Javaheri

Subjects
candida vulvovaginitis, candida albicans, pregnancy, pcr-rflp, Medicine, Medicine (General), R5-920
Abstract

Background and Objective: Candida species are the second most common cause of vaginitis in worldwide after bacterial agents. This study was performed to determine the etiological factors of Candida vulvovaginitis in pregnant women. Methods: This descriptive-analytical study, was performed on 100 pregnant women with vaginal discomfort that referring to gynecologic and obstetric clinics of the Sanandaj Social Security Hospital, Kurdistan province, Iran during 2016. After obtaining informed consent and collecting background information using a questionnaire, the patients were examined by a specialist physician and samples were collected. Identification of isolates was done based on colony color and also using PCR-restriction fragment length polymorphism (PCR-RFLP) method. Results: Candida vulvovaginitis was seen in 29% of women. Candida albicans were the most common cause of the disease (86.2%) followed by Candida paraposilosis (10.43%) and Candida glabrat (45.3%) . There was no significant relationship between diabetes and candida vulvovaginitis. There was a significant relationship between the history of antibiotic usage, age over 35 and third trimester of pregnancy with Candida vulvaginitis (P

Published
2020

42. Descriptive comparison of admission characteristics between pandemic waves and multivariable analysis of the association of the Alpha variant (B.1.1.7 lineage) of SARS-CoV-2 with disease severity in inner London

Author

Keith Morris, Judith Breuer, NgeeKeong Tan, Eric Witele, Sophie Hunter, Monica Panca, Aleks Marek, Paul Flowers, Gaia Nebbia, Sam Haldenby, Jacqui Prieto, Gee Yen Shin, Fiona Mapp, Andrew Copas, Mark Hopkins, Oliver Stirrup, Adam Witney, Kenneth Laing, May Rabuya, Vasa Curcin, Alison Holmes, Mohammad Raza, Wenjuan Wang, Rachel Williams, David Robertson, Julie Samuel, Rory Gunson, Helen Wheeler, Alexander J Keeley, Paul Randell, Cariad Evans, Tabassum Khan, Michelle Ramsay, Darren Smith, James Price, Sarah Francis, Shazaad Ahmad, Finola Higgins, Eleni Nastouli, Abhinav Kumar, Katie Johnson, Sharon Glaysher, Scott Elliott, Rebecca Gregory, Matthew D Parker, Helen Umpleby, Emanuela Pelosi, Emma Thomson, Anna Riddell, Yanzhong Wang, David Harrington, Alexandra Bailey, Nikunj Mahida, Charlotte Williams, Tanzina Haque, David G Partridge, Yusri Taha, Adrienn Angyal, Catherine Houlihan, James Shepherd, Hayley Colton, Chris Davis, Adela Alcolea-Medina, Themoula Charalampous, Beatrix Kele, Irene Monahan, Guy Mollett, Sunando Roy, Joshua Taylor, Sophie Weller, Eleri Wilson-Davies, Joseph Hughes, Tabitha Mahungu, Cassie Pope, Samuel Robson, Kordo Saeed, Luke Snell, James Blackstone, Leanne Hockey, Georgia Marley, Christine Peters, Flavia Flaviani, Bindi Patel, Rahul Batra, Jennifer Hart, Nadua Bayzid, Marius Cotic, Luke Green, Amy State, Alison Cope, Peijun Zhang, Max Whiteley, Marta Gallis Ramalho, Stella Christou, Paige Wolverson, Joe Heffer, Nikki Smith, Salman Goudarzi, Kate Cook, Katie Loveson, Buddhini Samaraweera, Stephen Aplin, Sarah Jeremiah, Matthew Harvey, Thea Sass, Dan Frampton, Matt Byott, Judith Heaney, Ana da Silva Filipe, Thushan de Silva, Jonathan Edgeworth, Luke B Snell, Leonardo de Jongh, Teresa Cutino-Moguel, Raghavendran Kulasegaran-Shylini, Claire E. Broad, Dola Owoyemi, Clare Coffey, Martina Cummins, Tyrra D’Souza, Emily Goldstein, Emilie Shepherd, Katherine Smollett, Alice Broos, Stephen Carmichael, Nicholas Suarez, Sreenu Vattipally, Ioulia Tsatsani, Jacqueline McTaggart, Stephanie McEnhill, Adela Medina, Jörg Saßmannshausen, Sulekha Gurung, Anu Augustine, Sid Mookerjee, Krystal Johnson, Thilipan Thaventhiran, Damien Mine, Isa Ahmad, Anitha Ramanathan, Anu Chawla, Alistair Derby, Becky Taylor, Charles Numbere, Jenifer Mason, Nicholas Machin, Julie Cawthorne, Ryan George, James Montgomery, Deborah McKew, Angela Cobb, Maria Leader, Shirelle Burton-Fanning, Lydia Taylor, Matthew Bashton, Matthew Crown, Matthew Loose, Patrick McClure, Mitch Clarke, Elaine Baxter, Carl Yates, Irfan Aslam, Vicki Fleming, Michelle Lister, Johnny Debebe, Nadine Holmes, Christopher Moore, Matt Carlile, Dianne Irish-Tavares, Mia De Mesa, Vicky Pang, Jelena Heaphy, Wendy Chatterton, Monika Pusok, Tranprit Saluja, Zahira Maqsood, Angie Williams, Debbie Devonport, Lucy Palinkas, Diane Thomlinson, Julie Booth, Ashok Dadrah, Amanda Symonds, Cassandra Craig, Benjamin B Lindsey, Benjamin H Foulkes, Stavroula F Louka, Phillip Ravencroft, Sharon Hsu, Nasar Ali, Rasha Raghei, Samantha E Hansford, Hailey R Hornsby, Phil Wade, Kay Cawthron, Maqsood Khan, Amber Ford, Imogen Wilson, Kate Harrington, Nic Tinker, Sally Nyinza, Adhyana Mahanama, Siona Silviera, Christopher Fearn, Claudia Cardosa Pereira, Vaz Malik, Gema Martinez-Garcia, Leila Hail, Ndifreke Atang, Helen Francis, Milica Rajkov, Rachel McComish, Alyson MacNeil, Alif Tamuri, and Stefan Piatek

Subjects
Medicine
Published
2022
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43. Impact of conflict and displacement on risk behaviours amongst people who inject drugs in Kabul, Afghanistan

Author

Todd, Catherine S, Nasir, Abdul, Stanekzai, Mohammad Raza, Fiekert, Katja, Sipsma, Heather L, Strathdee, Steffanie A, and Vlahov, David

Subjects
Policy and Administration, Human Society, Substance Misuse, Drug Abuse (NIDA only), Good Health and Well Being, Adult, Afghan Campaign 2001-, Afghanistan, Follow-Up Studies, Humans, Male, Refugees, Risk-Taking, Substance Abuse, Intravenous, Young Adult, Medical and Health Sciences, Studies in Human Society, Psychology and Cognitive Sciences, Substance Abuse, Public health, Policy and administration
Abstract

BACKGROUND: Theoretical work posits that drug-related risk behaviour increases during armed conflict; however, few studies have been conducted in conflict settings. The objective of this analysis is to determine whether conflict or local displacement impact risk behaviours among people who inject drugs (PWID) in Kabul, Afghanistan. METHODS: Consenting PWIDs aged ≥18 years completed interviews at 3, 6, 9, 12, 18, and 24 months of follow-up. Quarters with peak conflict or local displacement exposure were defined and associations with injecting drug use and sexual risk behaviours analysed with generalized estimating equations. RESULTS: Of 483 PWID enrolled, 385 completed ≥1 follow-up visit (483.8 person-years) between 2007 and 2009. All participants were male, with 35% initiating injecting as a refugee. Sharing syringes (Odds Ratio (OR))=8.53, 95% Confidence Interval (CI): 2.58 – 28.2) and sexually transmitted infection (STI) symptoms (OR=1.72, 95% CI: 1.00 – 2.96) increased significantly during peak conflict quarters, while odds of STI symptoms (OR=0.06, 95% CI: 0.02 – 0.20) and arrest (OR=0.61, 95% CI: 0.40 – 0.93) were significantly lower during periods of displacement. CONCLUSION: Syringe sharing significantly increased during peak conflict periods amongst PWID in Kabul. Programming should include instruction for coping with conflict and prepare clients for harm reduction needs during conflict.

Published
2016

44. Microalgae as Bio-Converters of Wastewater into Biofuel and Food

Author

Siddiqui, Mohammad Raza, Miranda, Ana, Mouradov, Aidyn, Jegatheesan, Jega V., Series Editor, Shu, Li, Series Editor, Lens, Piet, Series Editor, Chiemchaisri, Chart, Series Editor, Pannirselvam, Muthu, editor, Griffin, Gregory, editor, Philip, Ligy, editor, Natarajan, Ashok, editor, and Hussain, Sajid, editor

Published
2019
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45. Hepatitis C and HIV incidence and harm reduction program use in a conflict setting: an observational cohort of injecting drug users in Kabul, Afghanistan

Author

Todd, Catherine S, Nasir, Abdul, Stanekzai, Mohammad Raza, Fiekert, Katja, Sipsma, Heather L, Vlahov, David, and Strathdee, Steffanie A

Subjects
Public Health, Health Sciences, Behavioral and Social Science, Hepatitis, Infectious Diseases, Sexually Transmitted Infections, Hepatitis - C, Prevention, Liver Disease, Clinical Research, Emerging Infectious Diseases, Drug Abuse (NIDA only), Chronic Liver Disease and Cirrhosis, HIV/AIDS, Substance Misuse, Digestive Diseases, 3.1 Primary prevention interventions to modify behaviours or promote wellbeing, Infection, Good Health and Well Being, Adult, Afghan Campaign 2001-, Afghanistan, Cohort Studies, Comorbidity, Drug Users, HIV Infections, Harm Reduction, Hepatitis C, Humans, Incidence, Male, Needle Sharing, Needle-Exchange Programs, Risk Factors, Risk-Taking, Substance Abuse, Intravenous, Injecting drug use, Armed conflict, Hepatitis C virus, HIV, Harm reduction, Public Health and Health Services, Substance Abuse, Health services and systems, Public health
Abstract

BackgroundArmed conflict may increase the risk of HIV and other pathogens among injecting drug users (IDUs); however, there are few prospective studies. This study aimed to measure incidence and potential predictors, including environmental events and needle and syringe distribution and collection program (NSP) use, of hepatitis C virus (HCV) and HIV among IDUs in Kabul, Afghanistan.MethodsConsenting adult IDUs completed interviews quarterly in year 1 and semi-annually in year 2 and HCV and HIV antibody testing semi-annually through the cohort period (November 2007-December 2009). Interviews detailed injecting and sexual risk behaviors, NSP service use, and conflict-associated displacement. Quarters with peak conflict or local displacement were identified based on literature review, and key events, including insurgent attacks and deaths, were reported with simple counts. Incidence and predictors of HCV and HIV were measured with Cox proportional hazards models.ResultsOf 483 IDUs enrolled, 385 completed one or more follow-up visits (483.8 person-years (p-y)). All participants were male with a median age of 28 years and a median duration of injecting of 2 years. Reported NSP use among the participants ranged from 59.9 to 70.5 % in the first year and was 48.4 and 55.4 % at 18 and 24 months, respectively. There were 41 confirmed deaths, with a crude death rate of 93.4/1000 p-y (95 % confidence interval (CI) 67.9-125) and overdose as the most common cause. HCV and HIV incidence were 35.6/100 p-y (95 % CI 28.3-44.6) and 1.5/100 p-y (95 % CI 0.6-3.3), respectively. Changing from injecting to smoking was protective for HCV acquisition (adjusted hazard ratio (AHR) = 0.53, 95 % CI 0.31-0.92), while duration of injecting (AHR = 1.09, 95 % CI 1.01-1.18/year) and sharing syringes (AHR = 10.09, 95 % CI 1.01-100.3) independently predicted HIV infection.ConclusionThere is high HCV incidence and high numbers of reported deaths among male Kabul IDUs despite relatively consistent levels of harm reduction program use; peak violence periods did not independently predict HCV and HIV risk. Programming should increase awareness of HCV transmission and overdose risks, prepare clients for harm reduction needs during conflict or other causes of displacement, and continue efforts to engage community and police force support.

Published
2015

46. The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

Author

Thushan I. de Silva, Guihai Liu, Benjamin B. Lindsey, Danning Dong, Shona C. Moore, Nienyun Sharon Hsu, Dhruv Shah, Dannielle Wellington, Alexander J. Mentzer, Adrienn Angyal, Rebecca Brown, Matthew D. Parker, Zixi Ying, Xuan Yao, Lance Turtle, Susanna Dunachie, Mala K. Maini, Graham Ogg, Julian C. Knight, Yanchun Peng, Sarah L. Rowland-Jones, Tao Dong, David M. Aanensen, Khalil Abudahab, Helen Adams, Alexander Adams, Safiah Afifi, Dinesh Aggarwal, Shazaad S.Y. Ahmad, Louise Aigrain, Adela Alcolea-Medina, Nabil-Fareed Alikhan, Elias Allara, Roberto Amato, Tara Annett, Stephen Aplin, Cristina V. Ariani, Hibo Asad, Amy Ash, Paula Ashfield, Fiona Ashford, Laura Atkinson, Stephen W. Attwood, Cressida Auckland, Alp Aydin, David J. Baker, Paul Baker, Carlos E. Balcazar, Jonathan Ball, Jeffrey C. Barrett, Magdalena Barrow, Edward Barton, Matthew Bashton, Andrew R. Bassett, Rahul Batra, Chris Baxter, Nadua Bayzid, Charlotte Beaver, Angela H. Beckett, Shaun M. Beckwith, Luke Bedford, Robert Beer, Andrew Beggs, Katherine L. Bellis, Louise Berry, Beatrice Bertolusso, Angus Best, Emma Betteridge, David Bibby, Kelly Bicknell, Debbie Binns, Alec Birchley, Paul W. Bird, Chloe Bishop, Rachel Blacow, Victoria Blakey, Beth Blane, Frances Bolt, James Bonfield, Stephen Bonner, David Bonsall, Tim Boswell, Andrew Bosworth, Yann Bourgeois, Olivia Boyd, Declan T. Bradley, Cassie Breen, Catherine Bresner, Judith Breuer, Stephen Bridgett, Iraad F. Bronner, Ellena Brooks, Alice Broos, Julianne R. Brown, Giselda Bucca, Sarah L. Buchan, David Buck, Matthew Bull, Phillipa J. Burns, Shirelle Burton-Fanning, Timothy Byaruhanga, Matthew Byott, Sharon Campbell, Alessandro M. Carabelli, James S. Cargill, Matthew Carlile, Silvia F. Carvalho, Anna Casey, Anibolina Castigador, Jana Catalan, Vicki Chalker, Nicola J. Chaloner, Meera Chand, Joseph G. Chappell, Themoula Charalampous, Wendy Chatterton, Yasmin Chaudhry, Carol M. Churcher, Gemma Clark, Phillip Clarke, Benjamin J. Cogger, Kevin Cole, Jennifer Collins, Rachel Colquhoun, Thomas R. Connor, Kate F. Cook, Jason Coombes, Sally Corden, Claire Cormie, Nicholas Cortes, Marius Cotic, Seb Cotton, Simon Cottrell, Lindsay Coupland, MacGregor Cox, Alison Cox, Noel Craine, Liam Crawford, Aidan Cross, Matthew R. Crown, Dorian Crudgington, Nicola Cumley, Tanya Curran, Martin D. Curran, Ana da Silva Filipe, Gavin Dabrera, Alistair C. Darby, Rose K. Davidson, Alisha Davies, Robert M. Davies, Thomas Davis, Daniela de Angelis, Elen De Lacy, Leonardo de Oliveira Martins, Johnny Debebe, Rebecca Denton-Smith, Samir Dervisevic, Rebecca Dewar, Jayasree Dey, Joana Dias, Donald Dobie, Matthew J. Dorman, Fatima Downing, Megan Driscoll, Louis du Plessis, Nichola Duckworth, Jillian Durham, Kirstine Eastick, Lisa J. Easton, Richard Eccles, Jonathan Edgeworth, Sue Edwards, Kate El Bouzidi, Sahar Eldirdiri, Nicholas Ellaby, Scott Elliott, Gary Eltringham, Leah Ensell, Michelle J. Erkiert, Marina Escalera Zamudio, Sarah Essex, Johnathan M. Evans, Cariad Evans, William Everson, Derek J. Fairley, Karlie Fallon, Arezou Fanaie, Ben W. Farr, Christopher Fearn, Theresa Feltwell, Lynne Ferguson, Laia Fina, Flavia Flaviani, Vicki M. Fleming, Sally Forrest, Ebenezer Foster-Nyarko, Benjamin H. Foulkes, Luke Foulser, Mireille Fragakis, Dan Frampton, Sarah Francois, Christophe Fraser, Timothy M. Freeman, Helen Fryer, Marc Fuchs, William Fuller, Kavitha Gajee, Katerina Galai, Abbie Gallagher, Eileen Gallagher, Michael D. Gallagher, Marta Gallis, Amy Gaskin, Bree Gatica-Wilcox, Lily Geidelberg, Matthew Gemmell, Iliana Georgana, Ryan P. George, Laura Gifford, Lauren Gilbert, Sophia T. Girgis, Sharon Glaysher, Emily J. Goldstein, Tanya Golubchik, Andrea N. Gomes, Sónia Gonçalves, Ian G. Goodfellow, Scott Goodwin, Salman Goudarzi, Marina Gourtovaia, Clive Graham, Lee Graham, Paul R. Grant, Luke R. Green, Angie Green, Jane Greenaway, Richard Gregory, Martyn Guest, Rory N. Gunson, Ravi K. Gupta, Bernardo Gutierrez, Sam T. Haldenby, William L. Hamilton, Samantha E. Hansford, Tanzina Haque, Kathryn A. Harris, Ian Harrison, Ewan M. Harrison, Jennifer Hart, John A. Hartley, William T. Harvey, Matthew Harvey, Mohammed O. Hassan-Ibrahim, Judith Heaney, Thomas Helmer, John H. Henderson, Andrew R. Hesketh, Jessica Hey, David Heyburn, Ellen E. Higginson, Verity Hill, Jack D. Hill, Rachel A. Hilson, Ember Hilvers, Matthew T.G. Holden, Amy Hollis, Christopher W. Holmes, Nadine Holmes, Alison H. Holmes, Richard Hopes, Hailey R. Hornsby, Myra Hosmillo, Catherine Houlihan, Hannah C. Howson-Wells, Jonathan Hubb, Hannah Huckson, Warwick Hughes, Joseph Hughes, Margaret Hughes, Stephanie Hutchings, Giles Idle, Chris J. Illingworth, Robert Impey, Dianne Irish-Tavares, Miren Iturriza-Gomara, Rhys Izuagbe, Chris Jackson, Ben Jackson, Leigh M. Jackson, Kathryn A. Jackson, David K. Jackson, Aminu S. Jahun, Victoria James, Keith James, Christopher Jeanes, Aaron R. Jeffries, Sarah Jeremiah, Andrew Jermy, Michaela John, Rob Johnson, Kate Johnson, Ian Johnston, Owen Jones, Sophie Jones, Hannah Jones, Christopher R. Jones, Neil Jones, Amelia Joseph, Sarah Judges, Gemma L. Kay, Sally Kay, Jon-Paul Keatley, Alexander J. Keeley, Anita Kenyon, Leanne M. Kermack, Manjinder Khakh, Stephen P. Kidd, Maimuna Kimuli, Stuart Kirk, Christine Kitchen, Katie Kitchman, Bridget A. Knight, Cherian Koshy, Moritz U.G. Kraemer, Sara Kumziene-Summerhayes, Dominic Kwiatkowski, Angie Lackenby, Kenneth G. Laing, Temi Lampejo, Cordelia F. Langford, Deborah Lavin, Andrew I. Lawton, Jack Lee, David Lee, Stefanie V. Lensing, Steven Leonard, Lisa J. Levett, Thanh Le-Viet, Jonathan Lewis, Kevin Lewis, Jennifier Liddle, Steven Liggett, Patrick J. Lillie, Michelle M. Lister, Rich Livett, Stephanie Lo, Nicholas J. Loman, Matthew W. Loose, Stavroula F. Louka, Katie F. Loveson, Sarah Lowdon, Hannah Lowe, Helen L. Lowe, Anita O. Lucaci, Catherine Ludden, Jessica Lynch, Ronan A. Lyons, Katrina Lythgoe, Nicholas W. Machin, George MacIntyre-Cockett, Andrew Mack, Ben Macklin, Alasdair Maclean, Emily Macnaughton, Pinglawathee Madona, Mailis Maes, Laurentiu Maftei, Adhyana I.K. Mahanama, Tabitha W. Mahungu, Daniel Mair, Joshua Maksimovic, Cassandra S. Malone, Daniel Maloney, Nikos Manesis, Robin Manley, Anna Mantzouratou, Angela Marchbank, Arun Mariappan, Inigo Martincorena, Rocio T. Martinez Nunez, Alison E. Mather, Patrick Maxwell, Megan Mayhew, Tamyo Mbisa, Clare M. McCann, Shane A. McCarthy, Kathryn McCluggage, Patrick C. McClure, J.T. McCrone, Martin P. McHugh, James P. McKenna, Caoimhe McKerr, Georgina M. McManus, Claire L. McMurray, Claire McMurray, Alan McNally, Lizzie Meadows, Nathan Medd, Oliver Megram, Mirko Menegazzo, Ian Merrick, Stephen L. Michell, Michelle L. Michelsen, Mariyam Mirfenderesky, Jeremy Mirza, Julia Miskelly, Emma Moles-Garcia, Robin J. Moll, Zoltan Molnar, Irene M. Monahan, Matteo Mondani, Siddharth Mookerjee, Christopher Moore, Jonathan Moore, Nathan Moore, Catherine Moore, Helen Morcrette, Sian Morgan, Mari Morgan, Matilde Mori, Arthur Morriss, Samuel Moses, Craig Mower, Peter Muir, Afrida Mukaddas, Florence Munemo, Robert Munn, Abigail Murray, Leanne J. Murray, Darren R. Murray, Manasa Mutingwende, Richard Myers, Eleni Nastouli, Gaia Nebbia, Andrew Nelson, Charlotte Nelson, Sam Nicholls, Jenna Nichols, Roberto Nicodemi, Kyriaki Nomikou, Justin O’Grady, Sarah O'Brien, Mina Odedra, Natasha Ohemeng-Kumi, Karen Oliver, Richard J. Orton, Husam Osman, xeine O'Toole, Nicole Pacchiarini, Debra Padgett, Andrew J. Page, Emily J. Park, Naomi R. Park, Surendra Parmar, David G. Partridge, David Pascall, Amita Patel, Bindi Patel, Steve Paterson, Brendan A.I. Payne, Sharon J. Peacock, Clare Pearson, Emanuela Pelosi, Benita Percival, Jon Perkins, Malorie Perry, Malte L. Pinckert, Steven Platt, Olga Podplomyk, Manoj Pohare, Marcus Pond, Cassie F. Pope, Radoslaw Poplawski, Jessica Powell, Jennifer Poyner, Liam Prestwood, Anna Price, James R. Price, Jacqui A. Prieto, David T. Pritchard, Sophie J. Prosolek, Georgia Pugh, Monika Pusok, Oliver G. Pybus, Hannah M. Pymont, Michael A. Quail, Joshua Quick, Clara Radulescu, Jayna Raghwani, Manon Ragonnet-Cronin, Lucille Rainbow, Diana Rajan, Shavanthi Rajatileka, Newara A. Ramadan, Andrew Rambaut, John Ramble, Paul A. Randell, Paul Randell, Liz Ratcliffe, Veena Raviprakash, Mohammad Raza, Nicholas M. Redshaw, Sara Rey, Nicola Reynolds, Alex Richter, David L. Robertson, Esther Robinson, Samuel C. Robson, Fiona Rogan, Stefan Rooke, Will Rowe, Sunando Roy, Steven Rudder, Chris Ruis, Steven Rushton, Felicity Ryan, Kordo Saeed, Buddhini Samaraweera, Christine M. Sambles, Roy Sanderson, Theo Sanderson, Fei Sang, Thea Sass, Emily Scher, Garren Scott, Carol Scott, Jasveen Sehmi, Sharif Shaaban, Divya Shah, Jessica Shaw, Ekaterina Shelest, James G. Shepherd, Liz A. Sheridan, Nicola Sheriff, Lesley Shirley, John Sillitoe, Siona Silviera, David A. Simpson, Aditi Singh, Dawn Singleton, Timofey Skvortsov, Tim J. Sloan, Graciela Sluga, Ken Smith, Kim S. Smith, Perminder Smith, Darren L. Smith, Louise Smith, Colin P. Smith, Nikki Smith, Katherine L. Smollett, Luke B. Snell, Thomas Somassa, Joel Southgate, Karla Spellman, Michael H. Spencer Chapman, Lewis G. Spurgin, Moira J. Spyer, Rachael Stanley, William Stanley, Thomas D. Stanton, Igor Starinskij, Joanne Stockton, Susanne Stonehouse, Nathaniel Storey, David J. Studholme, Malur Sudhanva, Emma Swindells, Yusri Taha, Ngee Keong Tan, Julian W. Tang, Miao Tang, Ben E.W. Taylor, Joshua F. Taylor, Sarah Taylor, Ben Temperton, Kate E. Templeton, Claire Thomas, Laura Thomson, Emma C. Thomson, Alicia Thornton, Scott A.J. Thurston, John A. Todd, Rachael Tomb, Lily Tong, Gerry Tonkin-Hill, M. Estee Torok, Jaime M. Tovar-Corona, Amy Trebes, Alexander J. Trotter, Ioulia Tsatsani, Robyn Turnbull, Katherine A. Twohig, Helen Umpleby, Anthony P. Underwood, Edith E. Vamos, Tetyana I. Vasylyeva, Sreenu Vattipally, Gabrielle Vernet, Barry B. Vipond, Erik M. Volz, Sarah Walsh, Dennis Wang, Ben Warne, Joanna Warwick-Dugdale, Elizabeth Wastnedge, Joanne Watkins, Louisa K. Watson, Sheila Waugh, Hermione J. Webster, Danni Weldon, Elaine Westwick, Thomas Whalley, Helen Wheeler, Mark Whitehead, Max Whiteley, Andrew Whitwham, Claudia Wierzbicki, Nicholas J. Willford, Lesley-Anne Williams, Rebecca Williams, Cheryl Williams, Chris Williams, Charlotte A. Williams, Rachel J. Williams, Thomas Williams, Catryn Williams, Kathleen A. Williamson, Eleri Wilson-Davies, Eric Witele, Karen T. Withell, Adam A. Witney, Paige Wolverson, Nick Wong, Trudy Workman, Victoria Wright, Derek W. Wright, Tim Wyatt, Sarah Wyllie, Li Xu-McCrae, Mehmet Yavus, Geraldine Yaze, Corin A. Yeats, Gonzalo Yebra, Wen C. Yew, Gregory R. Young, Jamie Young, Alex E. Zarebski, Peijun Zhang, J. Kenneth Baillie, Malcolm G. Semple, Peter J.M. Openshaw, Gail Carson, Beatrice Alex, Petros Andrikopoulos, Benjamin Bach, Wendy S. Barclay, Debby Bogaert, Kanta Chechi, Graham S. Cooke, Annemarie B. Docherty, Gonçalo dos Santos Correia, Marc-Emmanuel Dumas, Jake Dunning, Tom Fletcher, Christopher A. Green, William Greenhalf, Julian L. Griffin, Rishi K. Gupta, Ewen M. Harrison, Julian A. Hiscox, Antonia Ying Wai Ho, Peter W. Horby, Samreen Ijaz, Saye Khoo, Paul Klenerman, Andrew Law, Matthew R. Lewis, Sonia Liggi, Wei Shen Lim, Lynn Maslen, Laura Merson, Alison M. Meynert, Mahdad Noursadeghi, Michael Olanipekun, Anthonia Osagie, Massimo Palmarini, Carlo Palmieri, William A. Paxton, Georgios Pollakis, Nicholas Price, Clark D. Russell, Vanessa Sancho-Shimizu, Caroline J. Sands, Janet T. Scott, Louise Sigfrid, Tom Solomon, Shiranee Sriskandan, David Stuart, Charlotte Summers, Olivia V. Swann, Zoltan Takats, Panteleimon Takis, Richard S. Tedder, A.A. Roger Thompson, Ryan S. Thwaites, Maria Zambon, Hayley Hardwick, Chloe Donohue, Fiona Griffiths, Wilna Oosthuyzen, Cara Donegan, Rebecca G. Spencer, Jo Dalton, Michelle Girvan, Egle Saviciute, Stephanie Roberts, Janet Harrison, Laura Marsh, Marie Connor, Sophie Halpin, Clare Jackson, Carrol Gamble, Daniel Plotkin, James Lee, Gary Leeming, Murray Wham, Sara Clohisey, Ross Hendry, James Scott-Brown, Victoria Shaw, Sarah E. McDonald, Seán Keating, Katie A. Ahmed, Jane A. Armstrong, Milton Ashworth, Innocent G. Asiimwe, Siddharth Bakshi, Samantha L. Barlow, Laura Booth, Benjamin Brennan, Katie Bullock, Benjamin W.A. Catterall, Jordan J. Clark, Emily A. Clarke, Sarah Cole, Louise Cooper, Helen Cox, Christopher Davis, Oslem Dincarslan, Chris Dunn, Philip Dyer, Angela Elliott, Anthony Evans, Lorna Finch, Lewis W.S. Fisher, Terry Foster, Isabel Garcia-Dorival, Philip Gunning, Catherine Hartley, Rebecca L. Jensen, Christopher B. Jones, Trevor R. Jones, Shadia Khandaker, Katharine King, Robyn T. Kiy, Chrysa Koukorava, Annette Lake, Suzannah Lant, Diane Latawiec, Lara Lavelle-Langham, Daniella Lefteri, Lauren Lett, Lucia A. Livoti, Maria Mancini, Sarah McDonald, Laurence McEvoy, John McLauchlan, Soeren Metelmann, Nahida S. Miah, Joanna Middleton, Joyce Mitchell, Ellen G. Murphy, Rebekah Penrice-Randal, Jack Pilgrim, Tessa Prince, Will Reynolds, P. Matthew Ridley, Debby Sales, Victoria E. Shaw, Rebecca K. Shears, Benjamin Small, Krishanthi S. Subramaniam, Agnieska Szemiel, Aislynn Taggart, Jolanta Tanianis-Hughes, Jordan Thomas, Erwan Trochu, Libby van Tonder, Eve Wilcock, J. Eunice Zhang, Lisa Flaherty, Nicole Maziere, Emily Cass, Alejandra Doce Carracedo, Nicola Carlucci, Anthony Holmes, Hannah Massey, Lee Murphy, Nicola Wrobel, Sarah McCafferty, Kirstie Morrice, Alan MacLean, Kayode Adeniji, Daniel Agranoff, Ken Agwuh, Dhiraj Ail, Erin L. Aldera, Ana Alegria, Sam Allen, Brian Angus, Abdul Ashish, Dougal Atkinson, Shahedal Bari, Gavin Barlow, Stella Barnass, Nicholas Barrett, Christopher Bassford, Sneha Basude, David Baxter, Michael Beadsworth, Jolanta Bernatoniene, John Berridge, Colin Berry, Nicola Best, Pieter Bothma, David Chadwick, Robin Brittain-Long, Naomi Bulteel, Tom Burden, Andrew Burtenshaw, Vikki Caruth, Duncan Chambler, Nigel Chee, Jenny Child, Srikanth Chukkambotla, Tom Clark, Paul Collini, Catherine Cosgrove, Jason Cupitt, Maria-Teresa Cutino-Moguel, Paul Dark, Chris Dawson, Phil Donnison, Sam Douthwaite, Andrew Drummond, Ingrid DuRand, Ahilanadan Dushianthan, Tristan Dyer, Chi Eziefula, Chrisopher Fegan, Adam Finn, Duncan Fullerton, Sanjeev Garg, Atul Garg, Effrossyni Gkrania-Klotsas, Jo Godden, Arthur Goldsmith, Elaine Hardy, Stuart Hartshorn, Daniel Harvey, Peter Havalda, Daniel B. Hawcutt, Maria Hobrok, Luke Hodgson, Anil Hormis, Michael Jacobs, Susan Jain, Paul Jennings, Agilan Kaliappan, Vidya Kasipandian, Stephen Kegg, Michael Kelsey, Jason Kendall, Caroline Kerrison, Ian Kerslake, Oliver Koch, Gouri Koduri, George Koshy, Shondipon Laha, Steven Laird, Susan Larkin, Tamas Leiner, Patrick Lillie, James Limb, Vanessa Linnett, Jeff Little, Mark Lyttle, Michael MacMahon, Emily MacNaughton, Ravish Mankregod, Huw Masson, Elijah Matovu, Katherine McCullough, Ruth McEwen, Manjula Meda, Gary Mills, Jane Minton, Kavya Mohandas, Quen Mok, James Moon, Elinoor Moore, Patrick Morgan, Craig Morris, Katherine Mortimore, Mbiye Mpenge, Rohinton Mulla, Michael Murphy, Megan Nagel, Thapas Nagarajan, Mark Nelson, Lillian Norris, Matthew K. O'Shea, Igor Otahal, Marlies Ostermann, Mark Pais, Selva Panchatsharam, Danai Papakonstantinou, Hassan Paraiso, Brij Patel, Natalie Pattison, Justin Pepperell, Mark Peters, Mandeep Phull, Stefania Pintus, Jagtur Singh Pooni, Tim Planche, Frank Post, David Price, Rachel Prout, Nikolas Rae, Henrik Reschreiter, Tim Reynolds, Neil Richardson, Mark Roberts, Devender Roberts, Alistair Rose, Guy Rousseau, Bobby Ruge, Brendan Ryan, Taranprit Saluja, Matthias L. Schmid, Aarti Shah, Prad Shanmuga, Anil Sharma, Anna Shawcross, Jeremy Sizer, Manu Shankar-Hari, Richard Smith, Catherine Snelson, Nick Spittle, Nikki Staines, Tom Stambach, Richard Stewart, Pradeep Subudhi, Tamas Szakmany, Kate Tatham, Jo Thomas, Chris Thompson, Robert Thompson, Ascanio Tridente, Darell Tupper-Carey, Mary Twagira, Nick Vallotton, Rama Vancheeswaran, Lisa Vincent-Smith, Shico Visuvanathan, Alan Vuylsteke, Sam Waddy, Rachel Wake, Andrew Walden, Ingeborg Welters, Tony Whitehouse, Paul Whittaker, Ashley Whittington, Padmasayee Papineni, Meme Wijesinghe, Martin Williams, Lawrence Wilson, Stephen Winchester, Martin Wiselka, Adam Wolverson, Daniel G. Wootton, Andrew Workman, Bryan Yates, and Peter Young

Subjects
Phylogenetics, Molecular biology, Immunology, Immune response, Virology, Science
Abstract

Summary: We identify amino acid variants within dominant SARS-CoV-2 T cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T cells assessed by IFN-γ and cytotoxic killing assays. Complete loss of T cell responsiveness was seen due to Q213K in the A∗01:01-restricted CD8+ ORF3a epitope FTSDYYQLY207-215; due to P13L, P13S, and P13T in the B∗27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17; and due to T362I and P365S in the A∗03:01/A∗11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK361-369. CD8+ T cell lines unable to recognize variant epitopes have diverse T cell receptor repertoires. These data demonstrate the potential for T cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T cell as well as humoral immunity.

Published
2021
Full Text
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49. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

Author

Bo Meng, Steven A. Kemp, Guido Papa, Rawlings Datir, Isabella A.T.M. Ferreira, Sara Marelli, William T. Harvey, Spyros Lytras, Ahmed Mohamed, Giulia Gallo, Nazia Thakur, Dami A. Collier, Petra Mlcochova, Lidia M. Duncan, Alessandro M. Carabelli, Julia C. Kenyon, Andrew M. Lever, Anna De Marco, Christian Saliba, Katja Culap, Elisabetta Cameroni, Nicholas J. Matheson, Luca Piccoli, Davide Corti, Leo C. James, David L. Robertson, Dalan Bailey, Ravindra K. Gupta, Samuel C. Robson, Nicholas J. Loman, Thomas R. Connor, Tanya Golubchik, Rocio T. Martinez Nunez, Catherine Ludden, Sally Corden, Ian Johnston, David Bonsall, Colin P. Smith, Ali R. Awan, Giselda Bucca, M. Estee Torok, Kordo Saeed, Jacqui A. Prieto, David K. Jackson, William L. Hamilton, Luke B. Snell, Catherine Moore, Ewan M. Harrison, Sonia Goncalves, Derek J. Fairley, Matthew W. Loose, Joanne Watkins, Rich Livett, Samuel Moses, Roberto Amato, Sam Nicholls, Matthew Bull, Darren L. Smith, Jeff Barrett, David M. Aanensen, Martin D. Curran, Surendra Parmar, Dinesh Aggarwal, James G. Shepherd, Matthew D. Parker, Sharon Glaysher, Matthew Bashton, Anthony P. Underwood, Nicole Pacchiarini, Katie F. Loveson, Kate E. Templeton, Cordelia F. Langford, John Sillitoe, Thushan I. de Silva, Dennis Wang, Dominic Kwiatkowski, Andrew Rambaut, Justin O’Grady, Simon Cottrell, Matthew T.G. Holden, Emma C. Thomson, Husam Osman, Monique Andersson, Anoop J. Chauhan, Mohammed O. Hassan-Ibrahim, Mara Lawniczak, Alex Alderton, Meera Chand, Chrystala Constantinidou, Meera Unnikrishnan, Alistair C. Darby, Julian A. Hiscox, Steve Paterson, Inigo Martincorena, Erik M. Volz, Andrew J. Page, Oliver G. Pybus, Andrew R. Bassett, Cristina V. Ariani, Michael H. Spencer Chapman, Kathy K. Li, Rajiv N. Shah, Natasha G. Jesudason, Yusri Taha, Martin P. McHugh, Rebecca Dewar, Aminu S. Jahun, Claire McMurray, Sarojini Pandey, James P. McKenna, Andrew Nelson, Gregory R. Young, Clare M. McCann, Scott Elliott, Hannah Lowe, Ben Temperton, Sunando Roy, Anna Price, Sara Rey, Matthew Wyles, Stefan Rooke, Sharif Shaaban, Mariateresa de Cesare, Laura Letchford, Siona Silveira, Emanuela Pelosi, Eleri Wilson-Davies, Myra Hosmillo, Áine O’Toole, Andrew R. Hesketh, Richard Stark, Louis du Plessis, Chris Ruis, Helen Adams, Yann Bourgeois, Stephen L. Michell, Dimitris Gramatopoulos, Jonathan Edgeworth, Judith Breuer, John A. Todd, Christophe Fraser, David Buck, Michaela John, Gemma L. Kay, Steve Palmer, Sharon J. Peacock, David Heyburn, Danni Weldon, Esther Robinson, Alan McNally, Peter Muir, Ian B. Vipond, John Boyes, Venkat Sivaprakasam, Tranprit Salluja, Samir Dervisevic, Emma J. Meader, Naomi R. Park, Karen Oliver, Aaron R. Jeffries, Sascha Ott, Ana da Silva Filipe, David A. Simpson, Chris Williams, Jane A.H. Masoli, Bridget A. Knight, Christopher R. Jones, Cherian Koshy, Amy Ash, Anna Casey, Andrew Bosworth, Liz Ratcliffe, Li Xu-McCrae, Hannah M. Pymont, Stephanie Hutchings, Lisa Berry, Katie Jones, Fenella Halstead, Thomas Davis, Christopher Holmes, Miren Iturriza-Gomara, Anita O. Lucaci, Paul Anthony Randell, Alison Cox, Pinglawathee Madona, Kathryn Ann Harris, Julianne Rose Brown, Tabitha W. Mahungu, Dianne Irish-Tavares, Tanzina Haque, Jennifer Hart, Eric Witele, Melisa Louise Fenton, Steven Liggett, Clive Graham, Emma Swindells, Jennifer Collins, Gary Eltringham, Sharon Campbell, Patrick C. McClure, Gemma Clark, Tim J. Sloan, Carl Jones, Jessica Lynch, Ben Warne, Steven Leonard, Jillian Durham, Thomas Williams, Sam T. Haldenby, Nathaniel Storey, Nabil-Fareed Alikhan, Nadine Holmes, Christopher Moore, Matthew Carlile, Malorie Perry, Noel Craine, Ronan A. Lyons, Angela H. Beckett, Salman Goudarzi, Christopher Fearn, Kate Cook, Hannah Dent, Hannah Paul, Robert Davies, Beth Blane, Sophia T. Girgis, Mathew A. Beale, Katherine L. Bellis, Matthew J. Dorman, Eleanor Drury, Leanne Kane, Sally Kay, Samantha McGuigan, Rachel Nelson, Liam Prestwood, Shavanthi Rajatileka, Rahul Batra, Rachel J. Williams, Mark Kristiansen, Angie Green, Anita Justice, Adhyana I.K. Mahanama, Buddhini Samaraweera, Nazreen F. Hadjirin, Joshua Quick, Radoslaw Poplawski, Leanne M. Kermack, Nicola Reynolds, Grant Hall, Yasmin Chaudhry, Malte L. Pinckert, Iliana Georgana, Robin J. Moll, Alicia Thornton, Richard Myers, Joanne Stockton, Charlotte A. Williams, Wen C. Yew, Alexander J. Trotter, Amy Trebes, George MacIntyre-Cockett, Alec Birchley, Alexander Adams, Amy Plimmer, Bree Gatica-Wilcox, Caoimhe McKerr, Ember Hilvers, Hannah Jones, Hibo Asad, Jason Coombes, Johnathan M. Evans, Laia Fina, Lauren Gilbert, Lee Graham, Michelle Cronin, Sara Kumziene-Summerhayes, Sarah Taylor, Sophie Jones, Danielle C. Groves, Peijun Zhang, Marta Gallis, Stavroula F. Louka, Igor Starinskij, Chris Jackson, Marina Gourtovaia, Gerry Tonkin-Hill, Kevin Lewis, Jaime M. Tovar-Corona, Keith James, Laura Baxter, Mohammad T. Alam, Richard J. Orton, Joseph Hughes, Sreenu Vattipally, Manon Ragonnet-Cronin, Fabricia F. Nascimento, David Jorgensen, Olivia Boyd, Lily Geidelberg, Alex E. Zarebski, Jayna Raghwani, Moritz U.G. Kraemer, Joel Southgate, Benjamin B. Lindsey, Timothy M. Freeman, Jon-Paul Keatley, Joshua B. Singer, Leonardo de Oliveira Martins, Corin A. Yeats, Khalil Abudahab, Ben E.W. Taylor, Mirko Menegazzo, John Danesh, Wendy Hogsden, Sahar Eldirdiri, Anita Kenyon, Jenifer Mason, Trevor I. Robinson, Alison Holmes, James Price, John A. Hartley, Tanya Curran, Alison E. Mather, Giri Shankar, Rachel Jones, Robin Howe, Sian Morgan, Elizabeth Wastenge, Michael R. Chapman, Siddharth Mookerjee, Rachael Stanley, Wendy Smith, Timothy Peto, David Eyre, Derrick Crook, Gabrielle Vernet, Christine Kitchen, Huw Gulliver, Ian Merrick, Martyn Guest, Robert Munn, Declan T. Bradley, Tim Wyatt, Charlotte Beaver, Luke Foulser, Sophie Palmer, Carol M. Churcher, Ellena Brooks, Kim S. Smith, Katerina Galai, Georgina M. McManus, Frances Bolt, Francesc Coll, Lizzie Meadows, Stephen W. Attwood, Alisha Davies, Elen De Lacy, Fatima Downing, Sue Edwards, Garry P. Scarlett, Sarah Jeremiah, Nikki Smith, Danielle Leek, Sushmita Sridhar, Sally Forrest, Claire Cormie, Harmeet K. Gill, Joana Dias, Ellen E. Higginson, Mailis Maes, Jamie Young, Michelle Wantoch, Dorota Jamrozy, Stephanie Lo, Minal Patel, Verity Hill, Claire M. Bewshea, Sian Ellard, Cressida Auckland, Ian Harrison, Chloe Bishop, Vicki Chalker, Alex Richter, Andrew Beggs, Angus Best, Benita Percival, Jeremy Mirza, Oliver Megram, Megan Mayhew, Liam Crawford, Fiona Ashcroft, Emma Moles-Garcia, Nicola Cumley, Richard Hopes, Patawee Asamaphan, Marc O. Niebel, Rory N. Gunson, Amanda Bradley, Alasdair Maclean, Guy Mollett, Rachel Blacow, Paul Bird, Thomas Helmer, Karlie Fallon, Julian Tang, Antony D. Hale, Louissa R. Macfarlane-Smith, Katherine L. Harper, Holli Carden, Nicholas W. Machin, Kathryn A. Jackson, Shazaad S.Y. Ahmad, Ryan P. George, Lance Turtle, Elaine O’Toole, Joanne Watts, Cassie Breen, Angela Cowell, Adela Alcolea-Medina, Themoula Charalampous, Amita Patel, Lisa J. Levett, Judith Heaney, Aileen Rowan, Graham P. Taylor, Divya Shah, Laura Atkinson, Jack C.D. Lee, Adam P. Westhorpe, Riaz Jannoo, Helen L. Lowe, Angeliki Karamani, Leah Ensell, Wendy Chatterton, Monika Pusok, Ashok Dadrah, Amanda Symmonds, Graciela Sluga, Zoltan Molnar, Paul Baker, Stephen Bonner, Sarah Essex, Edward Barton, Debra Padgett, Garren Scott, Jane Greenaway, Brendan A.I. Payne, Shirelle Burton-Fanning, Sheila Waugh, Veena Raviprakash, Nicola Sheriff, Victoria Blakey, Lesley-Anne Williams, Jonathan Moore, Susanne Stonehouse, Louise Smith, Rose K. Davidson, Luke Bedford, Lindsay Coupland, Victoria Wright, Joseph G. Chappell, Theocharis Tsoleridis, Jonathan Ball, Manjinder Khakh, Vicki M. Fleming, Michelle M. Lister, Hannah C. 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Subjects
SARS-CoV-2, COVID-19, antibody escape, neutralizing antibodies, infectivity, spike mutation, Biology (General), QH301-705.5
Abstract

Summary: We report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike ΔH69/V70 in multiple independent lineages, often occurring after acquisition of receptor binding motif replacements such as N439K and Y453F, known to increase binding affinity to the ACE2 receptor and confer antibody escape. In vitro, we show that, although ΔH69/V70 itself is not an antibody evasion mechanism, it increases infectivity associated with enhanced incorporation of cleaved spike into virions. ΔH69/V70 is able to partially rescue infectivity of spike proteins that have acquired N439K and Y453F escape mutations by increased spike incorporation. In addition, replacement of the H69 and V70 residues in the Alpha variant B.1.1.7 spike (where ΔH69/V70 occurs naturally) impairs spike incorporation and entry efficiency of the B.1.1.7 spike pseudotyped virus. Alpha variant B.1.1.7 spike mediates faster kinetics of cell-cell fusion than wild-type Wuhan-1 D614G, dependent on ΔH69/V70. Therefore, as ΔH69/V70 compensates for immune escape mutations that impair infectivity, continued surveillance for deletions with functional effects is warranted.

Published
2021
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