Assessment of COVID-19 intervention strategies in the Nordic countries using genomic epidemiology
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ABSTRACT:
SUBMITTER: Duchene S
PROVIDER: S-EPMC8755353 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundIn late December, 2019, patients presenting with viral pneumonia due to an unidentified microbial agent were reported in Wuhan, China. A novel coronavirus was subsequently identified as the causative pathogen, provisionally named 2019 novel coronavirus (2019-nCoV). As of Jan 26, 2020, more than 2000 cases of 2019-nCoV infection have been confirmed, most of which involved people living in or visiting Wuhan, and human-to-human transmission has been confirmed.MethodsWe did next-generation sequencing of samples from bronchoalveolar lavage fluid and cultured isolates from nine inpatients, eight of whom had visited the Huanan seafood market in Wuhan. Complete and partial 2019-nCoV genome sequences were obtained from these individuals. Viral contigs were connected using Sanger sequencing to obtain the full-length genomes, with the terminal regions determined by rapid amplification of cDNA ends. Phylogenetic analysis of these 2019-nCoV genomes and those of other coronaviruses was used to determine the evolutionary history of the virus and help infer its likely origin. Homology modelling was done to explore the likely receptor-binding properties of the virus.FindingsThe ten genome sequences of 2019-nCoV obtained from the nine patients were extremely similar, exhibiting more than 99·98% sequence identity. Notably, 2019-nCoV was closely related (with 88% identity) to two bat-derived severe acute respiratory syndrome (SARS)-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, collected in 2018 in Zhoushan, eastern China, but were more distant from SARS-CoV (about 79%) and MERS-CoV (about 50%). Phylogenetic analysis revealed that 2019-nCoV fell within the subgenus Sarbecovirus of the genus Betacoronavirus, with a relatively long branch length to its closest relatives bat-SL-CoVZC45 and bat-SL-CoVZXC21, and was genetically distinct from SARS-CoV. Notably, homology modelling revealed that 2019-nCoV had a similar receptor-binding domain structure to that of SARS-CoV, despite amino acid variation at some key residues.Interpretation2019-nCoV is sufficiently divergent from SARS-CoV to be considered a new human-infecting betacoronavirus. Although our phylogenetic analysis suggests that bats might be the original host of this virus, an animal sold at the seafood market in Wuhan might represent an intermediate host facilitating the emergence of the virus in humans. Importantly, structural analysis suggests that 2019-nCoV might be able to bind to the angiotensin-converting enzyme 2 receptor in humans. The future evolution, adaptation, and spread of this virus warrant urgent investigation.FundingNational Key Research and Development Program of China, National Major Project for Control and Prevention of Infectious Disease in China, Chinese Academy of Sciences, Shandong First Medical University.
| S-EPMC7159086 | biostudies-literature
Project description:Comparison of leaves from potato grown in different fields during 2018 and 2019
2024-08-12 | PXD026690 | Pride
Project description:The coronavirus disease 2019 (COVID-19) pandemic was one of the significant causes of death worldwide in 2020. The disease is caused by severe acute coronavirus syndrome (SARS) coronavirus 2 (SARS-CoV-2), an RNA virus of the subfamily Orthocoronavirinae related to 2 other clinically relevant coronaviruses, SARS-CoV and MERS-CoV. Like other coronaviruses and several other viruses, SARS-CoV-2 originated in bats. However, unlike other coronaviruses, SARS-CoV-2 resulted in a devastating pandemic. The SARS-CoV-2 pandemic rages on due to viral evolution that leads to more transmissible and immune evasive variants. Technology such as genomic sequencing has driven the shift from syndromic to molecular epidemiology and promises better understanding of variants. The COVID-19 pandemic has exposed critical impediments that must be addressed to develop the science of pandemics. Much of the progress is being applied in the developed world. However, barriers to the use of molecular epidemiology in low- and middle-income countries (LMICs) remain, including lack of logistics for equipment and reagents and lack of training in analysis. We review the molecular epidemiology literature to understand its origins from the SARS epidemic (2002-2003) through influenza events and the current COVID-19 pandemic. We advocate for improved genomic surveillance of SARS-CoV and understanding the pathogen diversity in potential zoonotic hosts. This work will require training in phylogenetic and high-performance computing to improve analyses of the origin and spread of pathogens. The overarching goals are to understand and abate zoonosis risk through interdisciplinary collaboration and lowering logistical barriers.
| S-EPMC9495640 | biostudies-literature
Project description:There is a rising global concern for the recently emerged novel coronavirus (2019-nCoV). Full genomic sequences have been released by the worldwide scientific community in the last few weeks to understand the evolutionary origin and molecular characteristics of this virus. Taking advantage of all the genomic information currently available, we constructed a phylogenetic tree including also representatives of other coronaviridae, such as Bat coronavirus (BCoV) and severe acute respiratory syndrome. We confirm high sequence similarity (>99%) between all sequenced 2019-nCoVs genomes available, with the closest BCoV sequence sharing 96.2% sequence identity, confirming the notion of a zoonotic origin of 2019-nCoV. Despite the low heterogeneity of the 2019-nCoV genomes, we could identify at least two hypervariable genomic hotspots, one of which is responsible for a Serine/Leucine variation in the viral ORF8-encoded protein. Finally, we perform a full proteomic comparison with other coronaviridae, identifying key aminoacidic differences to be considered for antiviral strategies deriving from previous anti-coronavirus approaches.
| S-EPMC7166773 | biostudies-literature
Project description:BackgroundFollowing the emergency approval of the coronavirus disease 2019 (COVID-19) vaccines, research into its vaccination hesitancy saw a substantial increase. However, the psychological behaviors associated with this hesitancy are still not completely understood. This study assessed the psychological antecedents associated with COVID-19 vaccination in the Arab population.MethodologyThe validated Arabic version of the 5C questionnaire was distributed online across various social media platforms in Arabic-speaking countries. The questionnaire had three sections, namely, socio-demographics, COVID-19 related infection and vaccination, and the 5C scale of vaccine psychological antecedents of confidence, complacency, constraints, calculation, and collective responsibility.ResultsIn total, 4,474 participants with a mean age of 32.48 ± 10.76 from 13 Arab countries made up the final sample, 40.8% of whom were male. Around 26.7% of the participants were found to be confident about the COVID-19 vaccination, 10.7% indicated complacency, 96.5% indicated they had no constraints, 48.8% had a preference for calculation and 40.4% indicated they had collective responsibility. The 5C antecedents varied across the studied countries with the confidence and collective responsibility being the highest in the United Arab Emirates (59.0% and 58.0%, respectively), complacency and constraints in Morocco (21.0% and 7.0%, respectively) and calculation in Sudan (60.0%). The regression analyses revealed that sex, age, educational degrees, being a health care professional, history of COVID-19 infection and having a relative infected or died from COVID-19 significantly predicted the 5C psychological antecedents by different degrees.ConclusionThere are wide psychological antecedent variations between Arab countries, and different determinants can have a profound effect on the COVID-19 vaccine's psychological antecedents.
| S-EPMC8629271 | biostudies-literature
Project description:ObjectivesDengue has been endemic in Southeast Asian countries for decades. There are few reports tracing the dynamics of dengue in real time. In this study, we generated hundreds of pathogen genomes to understand the genomic epidemiology of an outbreak in a hyper-endemic area of dengue.MethodsWe leveraged whole-genome short-read sequencing (PE150) to generate genomes of the dengue virus and investigated the genomic epidemiology of a dengue virus transmission in a mesoscale outbreak in Shantou, China, in 2019.ResultsThe outbreak was sustained from July to December 2019. The total accumulated number of laboratory-confirmed cases was 944. No gender bias or fatalities were recorded. Cambodia and Singapore were the main sources of imported dengue cases (74.07%, n = 20). A total of 284 dengue virus strains were isolated, including 259 DENV-1, 24 DENV-2, and 1 DENV-3 isolates. We generated the entire genome of 252 DENV isolates (229 DENV-1, 22 DENV-2, and 1 DENV-3), which represented 26.7% of the total cases. Combined epidemiological and phylogenetic analyses indicated multiple independent introductions. The internal transmission evaluations and transmission network reconstruction supported the inference of phylodynamic analysis, with high Bayes factor support in BSSVS analysis. Two expansion founders and transmission chains were detected in CCH and LG of Shantou.ConclusionsWe observed the instant effects of genomic epidemiology in monitoring the dynamics of DENV and highlighted its prospects for real-time tracing of outbreaks of other novel agents in the future.
| S-EPMC10374217 | biostudies-literature
Project description:Tuberculosis (TB) is one of the top 10 causes of death globally and the leading cause of death by a single infectious pathogen. The World Health Organization (WHO) has declared the End TB Strategy, which targets a 90% reduction in the incidence rate by the year 2035 compared to the level in the year 2015. In this work, a TB model is considered to understand the transmission dynamics in the top three TB burden countries-India, China, and Indonesia. Country-specific epidemiological parameters were identified using data reported by the WHO. If India and Indonesia succeed in enhancing their treatment protocols and increase treatment and treatment success rate to that of China, the incidence rate could be reduced by 65.99% and 68.49%, respectively, by the end of 2035. Evidently, complementary interventions are essential to achieve the WHO target. Our analytical approach utilizes optimal control theory to obtain time-dependent nonpharmaceutical and latent case finding controls. The objective functional of the optimal control problem includes a payoff term reflecting the goal set by WHO. Appropriate combinations of control strategies are investigated. Based on the results, gradual enhancement and continuous implementation of intervention measures are recommended in each country.
| S-EPMC7144981 | biostudies-literature
Project description:This SHEA white paper identifies knowledge gaps and challenges in healthcare epidemiology research related to coronavirus disease 2019 (COVID-19) with a focus on core principles of healthcare epidemiology. These gaps, revealed during the worst phases of the COVID-19 pandemic, are described in 10 sections: epidemiology, outbreak investigation, surveillance, isolation precaution practices, personal protective equipment (PPE), environmental contamination and disinfection, drug and supply shortages, antimicrobial stewardship, healthcare personnel (HCP) occupational safety, and return to work policies. Each section highlights three critical healthcare epidemiology research questions with detailed description provided in supplementary materials. This research agenda calls for translational studies from laboratory-based basic science research to well-designed, large-scale studies and health outcomes research. Research gaps and challenges related to nursing homes and social disparities are included. Collaborations across various disciplines, expertise and across diverse geographic locations will be critical.
| S-EPMC8160487 | biostudies-literature
Project description:Background/purposeWe aimed to describe the epidemiology of trauma activations and variations in injury patterns, injury severity, and hospital length-of-stay for injured children in Los Angeles (LA) County during the coronavirus-disease-19 (COVID-19) pandemic.MethodsWe conducted a retrospective cross-sectional study of children aged < 18-years evaluated in 15 trauma centers from 2019 to 2020 and entered in the LA County trauma registry. We defined 01/01/2019-03/18/2020 as pre-pandemic and 03/19/2020-12/31/2020 as the pandemic period. Our primary outcome was pediatric trauma activations. We analyzed demographic and clinical data, including types and severity of injuries sustained. We conducted unadjusted bivariate analyzes of injury patterns between periods. Segmented linear regression models were used to test rates (per 100,000 LA County children) of trauma activations pre-pandemic versus the pandemic period.ResultsWe studied 4399 children with trauma activations, 2695 of which occurred pre-pandemic and 1701 in the pandemic period. Motor vehicle collisions, gunshot wounds, and burns increased during the pandemic (all p-values< 0.05), while sports injuries decreased (p < 0.001). Median injury severity scores (p = 0.323) and Glasgow Coma Scales (p = 0.558) did not differ between periods, however mortality (p = 0.023) increased during the pandemic. Segmented linear regression estimates demonstrated that rates of trauma activations pre-pandemic were similar to the pandemic period (p = 0.384).ConclusionPediatric trauma activations in LA County did not significantly differ during the COVID-19 pandemic, but types and severity of injuries varied between pre-pandemic and pandemic periods. With lockdown restrictions being lifted and novel SARS-CoV-2 variants circulating, our investigation describes this recent epidemiologic phenomenon to aid future preparation for healthcare systems.Level of evidenceLevel III TYPE OF STUDY: Retrospective cross-sectional study.
| S-EPMC8500847 | biostudies-literature
Project description:BackgroundCare homes are vulnerable to widespread transmission of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) with poor outcomes for staff and residents. Infection control interventions in care homes need to not only be effective in containing the spread of coronavirus disease 2019 (COVID-19) but also feasible to implement in this special setting which is both a healthcare institution and a home.MethodsWe developed an agent-based model that simulates the transmission dynamics of COVID-19 via contacts between individuals, including residents, staff members, and visitors in a care home setting. We explored a representative care home in Scotland in our base case and explore other care home setups in an uncertainty analysis. We evaluated the effectiveness of a range of intervention strategies in controlling the spread of COVID-19.ResultsIn the presence of the reference interventions that have been implemented in many care homes, including testing of new admissions, isolation of symptomatic residents, and restricted public visiting, routine testing of staff appears to be the most effective and practical approach. Routine testing of residents is no more effective as a reference strategy while routine testing of both staff and residents only shows a negligible additive effect. Modeling results are very sensitive to transmission probability per contact, but the qualitative finding is robust to varying parameter values in our uncertainty analysis.ConclusionsOur model predictions suggest that routine testing should target staff in care homes in conjunction with adherence to strict hand hygiene and using personal protective equipment to reduce risk of transmission per contact.
| S-EPMC7783094 | biostudies-literature