The ARTIC protocol uses a multiplexed PCR approach with two primer pools tiling the entire SARS-CoV-2 genome. Primer pool updates are necessary for accurate amplicon sequencing of evolving SARS-CoV-2 variants with novel mutations. The suitability of the ARTIC V4 and updated V4.1 primer scheme was assessed using whole genome sequencing of Omicron from clinical samples using Oxford Nanopore Technology. Analysis of Omicron BA.1 genomes revealed that 93.22% of clinical samples generated improved genome coverage at 50x read depth with V4.1 primers when compared to V4 primers. Additionally, the V4.1 primers improved coverage of BA.1 across amplicons 76 and 88, which resulted in the detection of the variant defining mutations G22898A, A26530G and C26577G. The Omicron BA.2 sub-variant (VUI-22JAN-01) replaced BA.1 as the dominant variant by March 2022, and analysis of 168 clinical samples showed reduced coverage across amplicons 15 and 75. Upon further interrogation of primer binding sites, a mutation at C4321T (present in 163/168, 97% of 30 samples) was identified as a possible cause of complete dropout of amplicon 15. Furthermore, two mutations were identified within the primer binding regions for amplicon 75: A22786C (present in 90% of samples) and C22792T (present in 12.5% of samples). Together, these mutations may result in reduced coverage of amplicon 75 and further primer updates would allow the identification of the two BA.2 defining mutations present in amplicon 75; A22688G and T22679C. This work highlights the need for ongoing surveillance of primer matches as circulating variants evolve and change.
BACKGROUND: With widespread transmission of the Omicron SARS-CoV-2 variant, reinfections have become increasingly common. Here, we explored the role hybrid immunity, primary infection severity, and variant predominance on the risk of reinfection and severe COVID-19 during periods of Omicron predominance in Mexico. METHODS: We analyzed reinfections in Mexico in individuals with ≥90 days from a previous primary infection using a national surveillance registry of SARS-CoV-2 cases from March 3rd, 2020, until August 13th, 2022. Immunity-generating events included primary infection, partial or full vaccination and vaccine boosting. Reinfections were matched by age and sex with controls with primary SARS-CoV-2 infection and negative RT-PCR or antigen test ≥90 days after infection to explore risk factors for reinfection and reinfection-associated severe COVID-19. We also explored the protective role of heterologous vs. homologous vaccine boosters against reinfection or severe COVID-19 in fully vaccinated individuals. RESULTS: We detected 231,202 SARS-CoV-2 reinfections in Mexico, with most occurring in unvaccinated individuals (41.55%). Over 207,623 reinfections occurred during periods of Omicron (89.8%), BA.1 (36.74%) and BA.5 (33.67%) subvariant predominance and a case-fatality rate of 0.22%. Vaccination protected against reinfection, without significant influence of the order of immunity-generating events and provided >90% protection against severe reinfections. Heterologous booster schedules were associated with ~11% and ~54% lower risk for reinfection and reinfection-associated severe COVID-19 respectively, modified by time-elapsed since the last immunity-generating event. CONCLUSIONS: SARS-CoV-2 reinfections have increased during periods of Omicron predominance. Hybrid immunity provides protection against reinfection and reinfection-associated severe COVID-19, with potential benefit from heterologous booster schemes.
Background: Research demonstrates that SARS-CoV-2 infection (COVID-19) among adults disproportionately impacts racial and ethnic minorities and those living in lower-income communities. Similar research in children is limited due, in part, to the relatively low incidence in children compared to adults. This analysis, conducted as part of the RECOVER Initiative, explores this question. Methods: Electronic health record (EHR) data from PEDSnet, a multi-institutional research network of pediatric healthcare organizations, were geocoded and linked to two indices of contextual social deprivation: the Area Deprivation Index and the Child Opportunity Index. Univariate statistics were employed to test the association between each index and COVID19 positivity among children ages 0-20 tested at one of six Childrens hospitals. Multivariate logistic regression was used to explore the relationship between these social context indices and racial disparities in positivity, controlling co-variates. Results: Both ADI and COI were significantly associated with COVID-19 positivity in univariate and adjusted models, particularly in the pre-delta and delta variant waves. ADI showed a stronger association. Higher rates of positivity were found for non-Hispanic Black, Hispanic, and multi-racial children compared to non-Hispanic White children. These racial disparities remained significant after control for either index and other variables. Conclusion: ADI and COI are significantly associated with COVID-19 test positivity in a population of children and adolescents tested in childrens hospital settings. These social contextual variables do not fully explain racial disparities arguing that racial disparities are not solely a reflection of socioeconomic status. Future disparities research should consider both race and social context.
The Polio eradication campaign has been set back substantially since 2020 due to the COVID-19 pandemic. Recent detections of poliovirus transmission in multiple high-income countries suggest suboptimal population immunity in many parts of the world even though polio vaccination has been included in routine childhood immunization for decades. We reviewed polio vaccination schedules and vaccine uptake in the Western Pacific Region countries and assessed the potential shortfall in population immunity against polio resurgence across these populations. In addition, we conducted a repeated cross-sectional study between 2021 and 2022 in the Western Pacific Region to understand factors contributing to polio vaccine hesitancy. Our results reveal potential shortfalls in population immunity against polio in Western Pacific Region and provide insights into how vaccination programs and campaigns can be strengthened to ensure continual progress towards polio eradication.
Short-term forecasts can provide predictions of how an epidemic will change in the near future and form a central part of outbreak mitigation and control. Renewal-equation based models are increasingly popular. They infer key epidemiological parameters from historical epidemiological data and forecast future epidemic dynamics without requiring complex mechanistic assumptions. However, these models typically ignore interaction between age-groups, partly due to challenges in parameterising a time varying interaction matrix. Social contact data collected regularly by the CoMix survey during the COVID-19 epidemic in England, provide a means to inform interaction between age-groups in real-time. We developed an age-specific forecasting framework and applied it to two age-stratified time-series: incidence of SARS-CoV-2 infection, estimated from a national infection and antibody prevalence survey; and, reported cases according to the UK national COVID-19 dashboard. Jointly fitting our model to social contact data from the CoMix study, we inferred a time-varying next generation matrix which we used to project infections and cases in the four weeks following each of 29 forecast dates between October 2021 and November 2022. We evaluated the forecasts using proper scoring rules and compared performance with three other models with alternative data and specifications alongside two naive baseline models. Overall, incorporating age-interaction improved forecasts of infections and the CoMix-data-informed model was the best performing model at time horizons between two and four weeks. However, this was not true when forecasting cases. We found that age-group-interaction was most important for predicting cases in children and older adults. The contact-data-informed models performed best during the winter months of 2020 - 2021, but performed comparatively poorly in other periods. We highlight challenges regarding the incorporation of contact data in forecasting and offer proposals as to how to extend and adapt our approach, which may lead to more successful forecasts in future.
Background Remote interventions known as telemental health care increased in use due to the COVID-19 pandemic when social distancing requirements were in place. Whilst there is some evidence regarding the cost-effectiveness of telemental health prior to the pandemic, there is a need for further evaluation due to the increase in remote care. Aims To systematically review the literature to explore whether remote mental health care interventions are cost-effective in terms of incremental cost per quality adjusted life year and in relation to condition specific outcomes compared to usual care or an alternative intervention. Method A multilayer search strategy was conducted to build on the searches of a previous systematic review, as well as including grey literature and economic models. Six databases (PubMed, EMBASE, Cochrane Central, PsychINFO, CINAHL, and EconLit) were searched for literature relating to the cost effectiveness of telemental health. Quality appraisal was conducted for all included studies, and findings were synthesised using narrative synthesis. Results 7386 studies were identified of which 59 met our inclusion criteria and were included in the synthesis of findings. 45 studies were rated as very good or excellent quality. Of the 59 included studies, 40 indicated that the telemental health intervention was cost-effective, whilst a further 16 suggested the intervention had potential to be cost-effective, but there was some uncertainty in the findings. Three studies reported that the intervention was not cost-effective. Conclusions This evidence will be used to inform practice in the UK as we respond to and recover from the COVID-19 pandemic.
Advances in the field of image classification using convolutional neural networks (CNNs) have greatly improved the accuracy of medical image diagnosis by radiologists. Numerous research groups have applied CNN methods to diagnose respiratory illnesses from chest x-rays, and have extended this work to prove the feasibility of rapidly diagnosing COVID-19 to high degrees of accuracy. One issue in previous research has been the use of datasets containing only a few hundred images of chest x-rays containing COVID-19, causing CNNs to overfit the image data. This leads to a lower accuracy when the model attempts to classify new images, as would be clinically expected of it. In this work, we present a model trained on the COVID-QU-Ex dataset, overall containing 33,920 chest x-ray images, with an equal share of COVID-19, Non-COVID pneumonia, and Normal images. The model itself is an ensemble of pre-trained CNNs (ResNet50, VGG19, VGG16) and GLCM textural features. It achieved a 98.34% binary classification accuracy (COVID-19/no COVID-19) on a balanced test dataset of 6581 chest x-rays, and 94.68% for distinguishing between COVID-19, Non-COVID pneumonia and normal chest x-rays. Also, we herein discuss the effects of dataset size, demonstrating that a 98.82% 3-class accuracy can be achieved using the model if the training dataset only contains a few thousand images, but that generalisability of the model suffers with such small datasets.
The begging of 2020 saw the development and trials of vaccines against Covid-19 at an unprecedented pace. The first half of 2021 has seen vaccine rollout in many countries, on the other hand, Immunity to covid-19 has exhibited to minimize the risk of having a severe infection and initiate an excellent degree against the disease. This study compares Anti-Spike IgG antibodies among vaccinated people with or without previous exposure to the coronavirus. To determine whether a single dose of sputnik V can produce significant antibody titer amongst previously infected cases and design vaccine dosage regimens accordingly. This study was performed at the Libyan biotechnology research Centre from August 2021 to December 2021. Blood samples were collected from 1811 adult males and females vaccinated with and without a history of exposure to covid-19. Previously infected individuals9 record was noted separately. Samples were immediately analyzed by Beckman Unicel Dxl 600, Access immunoassay system. Data were analyzed using GraphPad Prism 9 Software. A P-value >0.5 was not significant. The Majority of candidates 60% of the total samples were males and on analysis, it was found that 72% of patients were seropositive, on the other hand, individuals who were vaccinated and have naive antibodies from the previous infection showed slightly higher immunological response rather than vaccinated patients without previous infected and this finding can help the policymakers to design a single-dose vaccine regimen for the former category. Keywords: Sputnik V, COVID-19, Antibody, Vaccine.
Pilot Clinical Trial to Explore Efficacy and Safety of Pyramax in Mild to Moderate COVID-19 Patients - Condition: COVID-19
Intervention: Drug: Pyramax
Sponsor: Shin Poong Pharmaceutical Co. Ltd.
Completed
Animation Supported COVID-19 Education - Condition: COVID-19 Pandemic
Intervention: Other: Animation-Supported Education
Sponsor: Siirt University
Completed
CareSuperb COVID-19 Antigen Test Usability - Condition: COVID-19
Intervention: Device: CareSuperb COVID-19 Antigen Home Test Kit
Sponsor: AccessBio, Inc.
Recruiting
Feasibility and Usability of COVID-19 Antigen RDTs in Uganda - Condition: COVID-19 Pandemic
Interventions: Diagnostic Test: PMC Sure Status COVID-19 Antigen Test; Diagnostic Test: Acon Flowflex COVID-19 Antigen Home Test
Sponsor: PATH
Not yet recruiting
SUNRISE-3: Efficacy and Safety of Bemnifosbuvir in High-Risk Outpatients With COVID-19 - Conditions: SARS CoV 2 Infection; COVID-19
Interventions: Drug: Bemnifosbuvir (BEM); Drug: Placebo
Sponsor: Atea Pharmaceuticals, Inc.
Recruiting
The Roles of Vitamin D and Microbiome in Children With Post-acute COVID-19 Syndromes (PACS) and Long COVID - Condition: Post-acute COVID-19 Syndromes
Interventions: Other: Vitamin D; Other: Placebo
Sponsor: China Medical University Hospital
Recruiting
A Study to Learn About Bivalent COVID-19 RNA Vaccine Candidate(s) in Healthy Infants and Children - Condition: COVID-19
Interventions: Biological: Bivalent BNT162b2 (original/Omicron BA.4/BA.5) 3 microgram dose; Biological: Bivalent BNT162b2 (original/Omicron BA.4/BA.5) 6 microgram dose; Biological: Bivalent BNT162b2 (original/Omicron BA.4/BA.5) 10 microgram dose; Biological: Bivalent BNT162b2 (original/Omicron BA.4/BA.5) 1 microgram dose
Sponsors: BioNTech SE; Pfizer
Not yet recruiting
Evaluation of an Integrative Medicine Outpatient Clinical Setting for Post-COVID-19 Patients - Conditions: COVID-19; Fatigue
Interventions: Behavioral: outpatient clinic with multimodal integrative medicine and naturopathy for post-COVID-19 patients; Other: waiting group
Sponsor: Universität Duisburg-Essen
Recruiting
Clinical Evaluation of the Panbio™ COVID-19/Flu A&B Rapid Panel Professional Use Product Using Mid-Turbinate Nasal Swabs - Conditions: COVID-19; Influenza A; Influenza Type B
Intervention: Diagnostic Test: Panbio™
Sponsor: Abbott Rapid Dx
Not yet recruiting
Efficacy of a Physical and Respiratory Rehabilitation Program for Patients With Persistent COVID-19 (SARS-CoV-2). - Conditions: SARS-CoV-2 Infection; COVID-19 Recurrent; Cognitive Dysfunction; Fatigue
Intervention: Other: COPERIA-REHAB
Sponsors: Fundacin Biomedica Galicia Sur; University of Vigo; Galician South Health Research Institute
Not yet recruiting
Evaluate the Efficacy and Safety of Azvudine in Preventing SARS-Cov-2 Infection in Household Contacts of Covid-19 - Condition: SARS-CoV-2 Infection
Interventions: Drug: Azvudine; Drug: Placebo
Sponsors: Shanghai Henlius Biotech; Shanghai Fosun Pharmaceutical Industrial Development Co. Ltd.; HeNan Sincere Biotech Co., Ltd
Not yet recruiting
Randomised Clinical Trial to Evaluate the Efficacy of an Online Cognitive Rehabilitation Programme (COPERIA-COG) for Patients With Persistent COVID-19 - Conditions: COVID-19; Neuro-Degenerative Disease; Psychological; SARS CoV 2 Infection
Intervention: Other: Sessions of cognitive stimulation
Sponsors: Fundacin Biomedica Galicia Sur; Centro de Investigación Biomédica en Red de Salud Mental; Galician South Health Research Institute
Not yet recruiting
VNS for Long-COVID-19 - Conditions: Post-COVID-19 Syndrome; Postural Tachycardia Syndrome; Dysautonomia
Interventions: Device: Non-invasive vagus nerve stimulation; Device: Sham Intervention
Sponsor: Icahn School of Medicine at Mount Sinai
Recruiting
Differential Diagnosis of Persistent COVID-19 by Artificial Intelligence - Conditions: COVID-19; Fatigue; Distress Respiratory Syndrome; Cognitive Dysfunction; COVID-19 Recurrent; SARS CoV 2 Infection
Intervention: Other: Experimental tests
Sponsors: Fundacin Biomedica Galicia Sur; University of Vigo; Galician South Health Research Institute
Not yet recruiting
Dietary Modulation of Gut Microbiota in Overweight/Obese Adolescents and COVID-19 Infection - Conditions: Health Behavior; Child Development; Adolescent Obesity
Interventions: Dietary Supplement: Probiotics; Behavioral: Counselling on healthy eating, physical activity, and psychosocial stimulation; Dietary Supplement: Placebo probiotics
Sponsors: Indonesia University; Gadjah Mada University; Universitas Airlangga; University of Melbourne; The Indonesia Endowment Funds for Education, Ministry of Finance Indonesia
Recruiting
Agent-based model using GPS analysis for infection spread and inhibition mechanism of SARS-CoV-2 in Tokyo - No abstract
Platelets in COVID-19 disease: friend, foe, or both? - No abstract
Effect of colonisation with Neisseria lactamica on cross-reactive anti-meningococcal B-cell responses: a randomised, controlled, human infection trial - No abstract
Functional proteomic profiling links deficient DNA clearance with increased mortality in individuals with severe COVID-19 pneumonia - No abstract
Cholinergic dysfunction in COVID-19: frantic search and hoping for the best - No abstract
Immune response and protective efficacy of the SARS-CoV-2 recombinant spike protein vaccine S-268019-b in mice - No abstract
Evaluation of action of steroid molecules on SARS-CoV-2 by inhibiting NSP-15, an endoribonuclease - No abstract
Co-ultramicronized palmitoylethanolamide/luteolin normalizes GABAB-ergic activity and cortical plasticity in long COVID-19 syndrome - No abstract
Ubiquitin specific peptidase 25 alleviates acute lung injury and suppresses the inflammatory response in lung epithelial cells - No abstract
Combining Computational and Experimental Evidence on the Activity of Antimalarial Drugs on Papain-Like Protease of SARS-CoV-2: A Repurposing Study - No abstract
PaxlovidTM Information From FDA and Guidance for AES Members - No abstract
Platelet in thrombo-inflammation: Unraveling new therapeutic targets - No abstract
Recombinant proteins of spike protein of SARS-CoV-2 with the Omicron receptor-binding domain induce production of highly Omicron-specific neutralizing antibodies - No abstract
B-cell lymphoma-2 family proteins-activated proteases as potential therapeutic targets for influenza A virus and severe acute respiratory syndrome coronavirus-2: Killing two birds with one stone? - No abstract
Common and rare variant associations with clonal haematopoiesis phenotypes - No abstract