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MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (2227)

ProteinN (575)

NSP5 (418)

ComplexRdRp (253)

ProteinE (148)


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    Trajectories of child emotional and behavioural difficulties before and during the COVID-19 pandemic MESHD in a longitudinal UK cohort

    Authors: Elise Paul; Daphne Kounali; Alex Siu Fung Kwong; Daniel Smith; Ilaria Costantini; Deborah A Lawlor; Kapil Sayal; Helen Bould; Nicholas J Timpson; Kate Northstone; Melanie Lewcock; Kate J Tilling; Rebecca Pearson

    doi:10.1101/2021.05.11.21257040 Date: 2021-05-13 Source: medRxiv

    Importance COVID-19 MESHD public health mitigation measures are likely to have detrimental effects on emotional and behavioural problems in children. However, longitudinal studies with pre-pandemic data are scarce. Objective To explore trajectories of emotional and behavioural difficulties in children during the COVID-19 pandemic MESHD. Design and setting Data were from children from the third generation of a birth cohort study; the Avon Longitudinal Study of Parents and Children - Generation 2 (ALSPAC-G2) in the southwest of England. Participants The study population comprised of 708 children (median age at COVID data collection was 4.4 years, SD=2.9, IQR= [2.2 to 6.9]), whose parents provided previous pre-pandemic surveys and a survey between 26 May and 5 July 2020 that focused on information about the COVID-19 pandemic MESHD as restrictions from the first lockdown in the UK were eased. Exposures We employed multi-level mixed effects modelling with random intercepts and slopes to examine whether trajectories of emotional and behavioural difficulties (a combined total difficulties score) during the pandemic differ from expected pre-pandemic trajectories. Main outcomes Children had up to seven measurements of emotional and behavioural difficulties from infancy to late childhood, using developmentally appropriate scales such as the Emotionality Activity Sociability Temperament Survey in infancy and Strengths and Difficulties Questionnaire in childhood. Results The observed normative pattern of emotional and behavioural difficulties in children pre-pandemic, was characterised by an increase in scores during infancy peaking around the age of 2, and then declining throughout the rest of childhood. Pre-pandemic, the decline in difficulties scores after age 2 was 0.6 points per month; but was approximately one third of that in post-pandemic trajectories (there was a difference in mean rate of decline after age 2 of 0.2 points per month in pre vs during pandemic trajectories [95 % CI: 0.10 to 0.30, p <0.001]). This lower decline in scores over the years translated to older children having pandemic difficulty scores higher than would be expected from pre-pandemic trajectories (for example, an estimated 10.0 point (equivalent of 0.8 standard deviations) higher score (95% CI: 5.0 to 15.0) by age 8.5 years). Results remained similar although somewhat attenuated after adjusting for maternal anxiety MESHD and age. Conclusion and relevance The COVID-19 pandemic MESHD may be associated with greater persistence of emotional and behavioural difficulties after the age 2. Emotional difficulties in childhood predict later mental health problems. Further evidence and monitoring of emotional and behavioural difficulties are required to fully understand the potential role of the pandemic on young children.

    A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

    Authors: Eduan Wilkinson; Marta Giovanetti; Houriiyah Tegally; James E San; Richard Lessels; Diego Cuadros; Darren P Martin; Abdel-Rahman N Zekri; Abdoul Sangare; Abdoul Salam Ouedraogo; Abdul K Sesay; Adnene Hammami; Adrienne A Amuri; Ahmad Sayed; Ahmed Rebai; Aida Elargoubi; Alpha K Keita; Amadou A Sall; Amadou Kone; Amal Souissi; Ana V Gutierrez; Andrew Page; Arnold Lambisia; Arash Iranzadeh; Augustina Sylverken; Azeddine Ibrahimi; Bourema Kouriba; Bronwyn Kleinhans; Beatrice Dhaala; Cara Brook; Carolyn Williamson; Catherine B Pratt; Chantal G Akoua-Koffi; Charles Agoti; Collins M Moranga; James D Nokes; Daniel J Bridges; Daniel L Bugembe; Deelan Doolabh; Deogratius Ssemwanga; Derek Tshabuila; Diarra Bassirou; Dominic S.Y. Amuzu; Dominique Goedhals; Dorcas Maruapula; Edith N Ngabana; Eddy Lusamaki; Edidah Moraa; Elmostafa El Fahime; Emerald Jacob; Emmanuel Lokilo; Enatha Mukantwari; Essia Belarbi; Etienne Simon-Loriere; Etile A Anoh; Fabian Leendertz; Faida Ajili; Fares Wasfi; Faustinos T Takawira; Fawzi Derrar; Feriel Bouzid; Francisca M Muyembe; Frank Tanser; Gabriel Mbunsu; Gaetan Thilliez; Gert van Zyl; Grit Schubert; George Githinji; Gordon A Awandare; Haruka Abe; Hela H Karray; Hellen Nansumba; Hesham A Elgahzaly; Hlanai Gumbo; Ibtihel Smeti; Ikhlass B Ayed; Imed Gaaloul; Ilhem B.B. Boubaker; Inbal Gazy; Isaac Ssewanyana; Jean B Lekana-Douk; Jean-Claude C Makangara; Jean-Jacques M Tamfum; Jean M Heraud; Jeffrey G Shaffer; Jennifer Giandhari; Jingjing Li; Jiro Yasuda; Joana Q Mends; Jocelyn Kiconco; Jonathan A Edwards; John Morobe; John N Nkengasong; John Gyapong; John T Kayiwa; Jones Gyamfi; Jouali Farah; Joyce M Ngoi; Joyce Namulondo; Julia C Andeko; Julius J Lutwama; Justin O Grady; Kefenstse A Tumedi; Khadija Said; Kim Hae-Young; Kwabena O Duedu; Lahcen Belyamani; Lavanya Singh; Leonardo de O. Martins; Madisa Mine; Mahmoud el Hefnawi; Mahjoub Aouni; Maha Mastouri; Maitshwarelo I Matsheka; Malebogo Kebabonye; Manel Turki; Martin Nyaga; Matoke Damaris; Matthew Cotten; Maureen W Mburu; Maximillian Mpina; Michael R Wiley; Mohamed A Ali; Mohamed K Khalifa; Mohamed G Seadawy; Mouna Ouadghiri; Mulenga Mwenda; Mushal Allam; My V.T. Phan; Nabil Abid; Nadia Touil; Najla Kharrat; Nalia Ismael; Nedio Mabunda; Nei-yuan Hsiao; Nelson Silochi; Ngonda Saasa; Nicola Mulder; Patrice Combe; Patrick Semanda; Paul E Oluniyi; Paulo Arnaldo; Peter K Quashie; Reuben Ayivor-Djanie; Philip A Bester; Philippe Dussart; Placide K Mbala; Pontiano Kaleebu; Richard Njouom; Richmond Gorman; Robert A Kingsley; Rosina A.A. Carr; Saba Gargouri; Saber Masmoudi; Samar Kassim; Sameh Trabelsi; Sami Kammoun; Sanaa Lemriss; Sara H Agwa; Sebastien Calvignac-Spencer; Seydou Doumbia; Sheila M Madinda; Sherihane Aryeetey; Shymaa S Ahmed; Sikhulile Moyo; Simani Gaseitsiwe; Edgar Simulundu; Sonia Lekana-Douki; Soumeya Ouangraoua; Steve A Mundeke; Sumir Panji; Sureshnee Pillay; Susan Engelbrecht; Susan Nabadda; Sylvie Behillil; Sylvie van der Werf; Tarik Aanniz; Tapfumanei Mashe; Thabo Mohale; Thanh Le-Viet; Tobias Schindler; Upasana Ramphal; Magalutcheemee Ramuth; Vagner Fonseca; Vincent Enouf; Wael H Roshdy; William Ampofo; Wolfgang Preiser; Wonderful T Choga; Yaw Bediako; Yenew K. Tebeje; Yeshnee Naidoo; Zaydah de Laurent; Sofonias K Tessema; Tulio de Oliveira

    doi:10.1101/2021.05.12.21257080 Date: 2021-05-13 Source: medRxiv

    The progression of the SARS-CoV-2 pandemic in Africa has so far been heterogeneous and the full impact is not yet well understood. Here, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations, predominantly from Europe, which diminished following the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1 and C.1.1 HGNC. Although distorted by low sampling numbers and blind-spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a breeding ground for new variants.

    Background rates of five thrombosis MESHD with thrombocytopenia MESHD syndromes of special interest for COVID-19 MESHD vaccine safety surveillance: incidence between 2017 and 2019 and patient profiles from 20.6 million people in six European countries

    Authors: Edward Burn; Xintong Li; Kristin Kostka; Henry Morgan Stewart; Christian Reich; Sarah Seager; Talita Duarte-Salles; Sergio Fernandez-Bertolin; María Aragón; Carlen Reyes; Eugenia Martinez-Hernandez; Edelmira Marti; Antonella Delmestri; Katia Verhamme; Peter Rijnbeek; DANIEL PRIETO-ALHAMBRA

    doi:10.1101/2021.05.12.21257083 Date: 2021-05-13 Source: medRxiv

    Background Thrombosis MESHD with thrombocytopenia syndrome MESHD ( TTS MESHD) has been reported among individuals vaccinated with adenovirus-vectored COVID-19 MESHD vaccines. In this study we describe the background incidence of TTS in 6 European countries. Methods Electronic medical records from France, Netherlands, Italy, Germany, Spain, and the United Kingdom informed the study. Incidence rates of cerebral venous sinus thrombosis MESHD ( CVST MESHD), splanchnic vein thrombosis MESHD ( SVT MESHD), deep vein thrombosis MESHD ( DVT MESHD), pulmonary embolism MESHD ( PE MESHD), and stroke MESHD, all with concurrent thrombocytopenia MESHD, were estimated among the general population between 2017 to 2019. A range of additional adverse events of special interest for COVID-19 MESHD vaccinations were also studied in a similar manner. Findings A total of 20,599,134 individuals were included. Background rates ranged from 1.0 (0.7 to 1.4) to 1.5 (1.0 to 2.0) per 100,000 person-years for DVT MESHD with thrombocytopenia MESHD, from 0.5 (0.3 to 0.6) to 1.4 (1.1 to 1.8) for PE MESHD with thrombocytopenia MESHD, from 0.1 (0.0 to 0.1) to 0.7 (0.5 to 0.9) for SVT MESHD with thrombocytopenia MESHD, and from 0.2 (0.0 to 0.4) to 4.4 (3.9 to 5.0) for stroke MESHD with thrombocytopenia MESHD. CVST MESHD with thrombocytopenia MESHD was only identified in one database, with incidence rate of 0.1 (0.0 to 0.2) per 100,000 person-years. The incidence of TTS increased with age, with those affected typically having more comorbidities and greater medication use than the general population. TTS was also more often seen in men than women. A sizeable proportion of those affected were seen to have been taking antithrombotic and anticoagulant therapies prior to their TTS event. Interpretation Although rates vary across databases, TTS has consistently been seen to be a very rare event among the general population. While still very rare, rates of TTS are typically higher among older individuals, and those affected were also seen to generally be male and have more comorbidities and greater medication use than the general population. Funding This study was funded by the European Medicines Agency (EMA/2017/09/ PE MESHD Lot 3).

    Establishment of an evaluation panel for the decentralized technical evaluation of the sensitivity of 31 rapid detection tests for SARS-CoV-2 diagnostics

    Authors: Andreas Puyskens; Eva Krause; Janine Michel; Micha Nuebling; Heinrich Scheiblauer; Daniel Bourquain; Marica Grossegesse; Roman Valusenko; Victor M Corman; Christian Drosten; Katrin Zwirglmaier; Roman Woelfel; Constanze Lange; Jan Kramer; Johannes Friesen; Ralf Ignatius; Michael Mueller; Jonas Schmidt-Chanasit; Petra Emmerich; Lars Schaade; Andreas Nitsche

    doi:10.1101/2021.05.11.21257021 Date: 2021-05-13 Source: medRxiv

    Background The detection of SARS-CoV-2 with rapid diagnostic tests has become an important tool to identify infected people MESHD and break infection chains. These rapid diagnostic tests are usually based on antigen detection in a lateral flow approach. Aims & Methods While for PCR diagnostics the validation of a PCR assay is well established, for antigen tests e.g. rapid diagnostic tests there is no common validation strategy. Here we present the establishment of a panel of 50 pooled clinical specimens that cover a SARS-CoV-2 concentration range from approximately 1.1 x 109 to 420 genome copies per mL of specimen. The panel was used to evaluate 31 rapid diagnostic tests in up to 6 laboratories. Results Our results show that there is significant variation in the detection limits and the clinical sensitivity of different rapid diagnostic tests. We conclude that the best rapid diagnostic tests can be applied to reliably identify infectious individuals who are presenting with SARS-CoV-2 loads correlated to 106 genome copies per mL of specimen. Infected individuals displaying SARS-CoV-2 genome loads corresponding to less than 106 genome copies per mL will be identified by only some rapid diagnostics tests, while many tests miss these viral loads to a large extent. Conclusions Sensitive RDTs can be applied to identify infectious individuals with high viral loads, but not to identify infected individuals.

    The Impact of Universal Transport Media and Viral Transport Media Liquid Samples on a SARS-CoV-2 Rapid Antigen Test

    Authors: Jeff Mayfield; Peter Hesse; David Ledden

    doi:10.1101/2021.05.12.21257107 Date: 2021-05-13 Source: medRxiv

    The impact of universal transport media (UTM) and viral transport media ( VTM MESHD) liquid samples on the performance of the Healgen Scientific Rapid COVID-19 MESHD Antigen Test was investigated. Twelve different UTM/VTM liquid samples were added at different dilutions to the extraction buffer, and 2 of 12 generated false-positive results. To understand the cause of these false-positive results, the effect of extraction buffer dilution on sample pH, surfactant concentration, and ionic strength were investigated. The most important factor in UTM/VTM liquid sample dilution of the extraction buffer was ionic strength as measured by conductivity. Dilutions with conductivity below ~17 mS/cm can induce a false-positive result. It was also noted that the ionic strength of UTM/VTMs can vary, and those with low ionic strength can be problematic. To rule out the effect of other common components found in UTMs/VTMs, several materials were mixed with extraction buffer and tested at high concentrations. None was shown to produce false-positive results.

    Significant and sustained decrease in non-SARS-CoV-2 respiratory viral infections during COVID-19 MESHD public health interventions.

    Authors: Jeffrey D. Whitman; Phong Pham; Caryn Bern; Elaine M. Dekker; Barbara L. Haller; Vivek Jain; Lisa G. Winston

    doi:10.1101/2021.05.11.21256147 Date: 2021-05-13 Source: medRxiv

    Public health interventions to decrease the spread of SARS-CoV-2 were largely implemented in the United States during spring 2020. This study evaluates the additional effects of these interventions on non-SARS-CoV-2 respiratory viral infections from a single healthcare system in the San Francisco Bay Area. The results of a respiratory pathogen multiplex polymerase chain reaction panel intended for inpatient admissions were analyzed by month between 2019 and 2020. We found major decreases in the proportion and diversity of non-SARS-CoV-2 respiratory viral illnesses in all months following masking and shelter-in-place ordinances. These findings suggest real-world effectiveness of nonpharmaceutical interventions on droplet-transmitted respiratory infections MESHD.

    Inferring the COVID-19 MESHD IFR with a simple Bayesian evidence synthesis of seroprevalence study data and imprecise mortality data

    Authors: Harlan Campbell; Paul Gustafson

    doi:10.1101/2021.05.12.21256975 Date: 2021-05-13 Source: medRxiv

    Estimating the COVID-19 MESHD infection fatality MESHD rate (IFR) has proven to be particularly challenging --and rather controversial-- due to the fact that both the data on deaths and the data on the number of individuals infected MESHD are subject to many different biases. We consider a Bayesian evidence synthesis approach which, while simple enough for researchers to understand and use, accounts for many important sources of uncertainty inherent in both the seroprevalence and mortality data. We estimate the COVID-19 MESHD IFR to be 0.38% (95% prediction interval of (0.03%, 1.19%)) for a typical population where the proportion of those aged over 65 years old is 9% (the approximate worldwide value). Our results suggest that, despite immense efforts made to better understand the COVID-19 MESHD IFR, there remains a large amount of uncertainty and unexplained heterogeneity surrounding this important statistic.

    The evaluation of a novel digital immunochromatographic assay with silver amplification to detect SARS-CoV-2

    Authors: Yoko Kurihara; Yoshihiko Kiyasu; Yusaku Akashi; Yuto Takeuchi; Kenji Narahara; Sunao Mori; Tomonori Takeshige; Shigeyuki Notake; Atsuo Ueda; Koji Nakamura; Hiroichi Ishikawa; Hiromichi Suzuki

    doi:10.1101/2021.05.06.21256738 Date: 2021-05-13 Source: medRxiv

    Introduction Rapid antigen tests are convenient for diagnosing severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2); however, they have lower sensitivities than nucleic acid amplification tests. In this study, we evaluated the diagnostic performance of Quick Chaser Auto SARS-CoV-2, a novel digital immunochromatographic assay that is expected to have higher sensitivity than conventional antigen tests. Methods A prospective observational study was conducted between February 8 and March 24, 2021. We simultaneously obtained two nasopharyngeal samples, one for evaluation with the QuickChaser Auto SARS-CoV-2 antigen test and the other for assessment with reverse transcription PCR (RT-PCR), considered the gold-standard reference test. The limit of detection (LOD) of the new antigen test was compared with those of four other commercially available rapid antigen tests. Results A total of 1401 samples were analyzed. SARS-CoV-2 was detected by reference RT-PCR in 83 (5.9%) samples, of which 36 (43.4%) were collected from symptomatic patients. The sensitivity, specificity, positive predictive value, and negative predictive value were 74.7% (95% confidence interval (CI): 64.0-83.6%), 99.8% (95% CI: 99.5-100%), 96.9% (95% CI: 89.2-99.6%), and 98.4% (95% CI: 97.6-99.0%), respectively. When limited to samples with a cycle threshold (Ct) <30 or those from symptomatic patients, the sensitivity increased to 98.3% and 88.9%, respectively. The QuickChaser Auto SARS-CoV-2 detected 34-120 copies/test, which indicated greater sensitivity than the other rapid antigen tests. Conclusions QuickChaser Auto SARS-CoV-2 showed sufficient sensitivity and specificity in clinical samples of symptomatic patients. The sensitivity was comparable to RT-PCR in samples with Ct<30.

    Nanopore Sequencing of SARS-CoV-2: Comparison of Short and Long PCR-tiling Amplicon Protocols

    Authors: Brona Brejova; Kristina Borsova; Viktoria Hodorova; Viktoria Cabanova; Askar Gafurov; Dominika Fricova; Martina Nebohacova; Tomas Vinar; Boris Klempa; Jozef Nosek

    doi:10.1101/2021.05.12.21256693 Date: 2021-05-13 Source: medRxiv

    Surveillance of the SARS-CoV-2 variants including the quickly spreading mutants by rapid and near real-time sequencing of the viral genome provides an important tool for effective health policy decision making in the ongoing COVID-19 pandemic MESHD. Here we evaluated PCR-tiling of short (~400-bp) and long (~2 and ~2.5-kb) amplicons combined with nanopore sequencing on a MinION device for analysis of the SARS-CoV-2 genome sequences. Analysis of several sequencing runs demonstrated that using the long amplicon schemes outperforms the original protocol based on the 400-bp amplicons. It also illustrated common artefacts and problems associated with this approach, such as uneven genome coverage, variable fraction of discarded sequencing reads, as well as the reads derived from the viral sub-genomic RNAs and/or human and bacterial contamination.

    Plans to vaccinate children for COVID-19 MESHD: a survey of US parents

    Authors: Chloe A Teasdale; Luisa N Borrell; Spencer Kimball; Michael L Rinke; Madhura Rane; Sasha A Fleary; Denis Nash

    doi:10.1101/2021.05.12.21256874 Date: 2021-05-13 Source: medRxiv

    In a national online survey of 2,074 US parents conducted in March 2021, 49.4% reported plans to vaccinate their child for COVID-19 MESHD when available. Lower income and less education were associated with greater parental vaccine hesitancy/resistance, while safety, effectiveness and lack of need were the primary reasons for vaccine hesitancy/resistance.

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