Editorial: "Source-tracking," molecular epidemiology and antigenic diversity of SARS-CoV-2 infections causing coronavirus disease 2019, COVID-19.
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ABSTRACT:
SUBMITTER: Narh CA
PROVIDER: S-EPMC9642110 | biostudies-literature | 2022
REPOSITORIES: biostudies-literature
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Editorial: "Source-tracking," molecular epidemiology and antigenic diversity of SARS-CoV-2 infections causing coronavirus disease 2019, COVID-19.
Narh Charles A CA Manickum Cordelia C Vajravelu Bathri B Zella Davide D Mosi Lydia L
Frontiers in genetics 20221025
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Project description:The emergence of 2019 novel coronavirus (2019-nCoV) is of global concern and might have emerged from RNA recombination among existing coronaviruses. CoV spike (S) protein which is crucial for receptor binding, membrane fusion via conformational changes, internalization of the virus, host tissue tropism and comprises crucial targets for vaccine development, remain largely uncharacterized. Therefore, the present study has been planned to determine the sequence variation, structural and antigenic divergence of S glycoprotein which may be helpful for the management of 2019-nCoV infection. The sequences of spike glycoprotein of 2019-nCoV and SARS coronavirus (SARS-CoV) were used for the comparison. The sequence variations were determined using EMBOSS Needle pairwise sequence alignment tools. The variation in glycosylation sites was predicted by NetNGlyc 1.0 and validated by N-GlyDE server. Antigenicity was predicted by NetCTL 1.2 and validated by IEDB Analysis Resource server. The structural divergence was determined by using SuperPose Version 1.0 based on cryo-EM structure of the SARS coronavirus spike glycoprotein. Our data suggests that 2019-nCoV is newly spilled coronavirus into humans in China is closely related to SARS-CoV, which has only 12.8% of difference with SARS-CoV in S protein and has 83.9% similarity in minimal receptor-binding domain with SARS-CoV. Addition of a novel glycosylation sites were observed in 2019-nCoV. In addition, antigenic analysis proposes that great antigenic differences exist between both the viral strains, but some of the epitopes were found to be similar between both the S proteins. In spite of the variation in S protein amino acid composition, we found no significant difference in their structures. Collectively, for the first time our results exhibit the emergence of human 2019-nCoV is closely related to predecessor SARS-CoV and provide the evidence that 2019-nCoV uses various novel glycosylation sites as SARS-CoV and may have a potential to become pandemic owing its antigenic discrepancy. Further, demonstration of novel Cytotoxic T lymphocyte epitopes may impart opportunities for the development of peptide based vaccine for the prevention of 2019-nCoV.
| S-EPMC7085496 | biostudies-literature
Project description:This article describes how coronavirus disease 2019 (COVID-19) health disparities relate to the social determinants of health and reviews the importance of a diverse nursing workforce prepared to advance social justice. The article reviews recommendations from the National Academy of Medicine and highlights practical strategies to promote diversity and social justice, including mentoring nurses from underrepresented backgrounds, amplifying diverse nursing voices, and leveraging the power of coalitions. In highlighting the interwoven impact of COVID-19 and demand for social change throughout 2020 to 2022, the article strives to move beyond the acute COVID-19 crisis to sustained social justice in health care.
| S-EPMC9618434 | biostudies-literature
Project description:BackgroundDengue is one of the newest emerging diseases in Nepal with increasing burden and geographic spread over the years. The main objective of this study was to explore the epidemiological patterns of dengue since its first outbreak (2006) to 2019 in Nepal.MethodsThis study is a retrospective analysis that covers the last 14 years (2006-2019) of reported dengue cases from Epidemiology Diseases Control Division (EDCD), Ministry of Health and Population, Government of Nepal. Reported cases were plotted over time and maps of reported case incidence were generated (from 2016 through 2019). An ecological analysis of environmental predictors of case incidence was conducted using negative binomial regression.ResultsWhile endemic dengue has been reported in Nepal since 2006, the case load has increased over time and in 2019 a total of 17 992 dengue cases were reported from 68 districts (from all seven provinces). Compared to the case incidence in 2016, incidence was approximately five times higher in 2018 [incidence rate ratio (IRR): 4.8; 95% confidence interval (CI) 1.5-15.3] and over 140 times higher in 2019 (IRR: 141.6; 95% CI 45.8-438.4). A one standard deviation increase in elevation was associated with a 90% decrease in reported case incidence (IRR: 0.10; 95% CI 0.01-0.20). However, the association between elevation and reported cases varied across the years. In 2018 there was a cluster of cases reported from high elevation Kaski District of Gandaki Province. Our results suggest that dengue infections are increasing in magnitude and expanding out of the lowland areas to higher elevations over time.ConclusionsThere is a high risk of dengue outbreak in the lowland Terai region, with increasing spread towards the mid-mountains and beyond as seen over the last 14 years. Urgent measures are required to increase the availability of diagnostics and resources to mitigate future dengue epidemics.
| S-EPMC8047528 | 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) decreased 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:Although several studies have associated Mycobacterium ulcerans (MU) infection, Buruli ulcer (BU), with slow moving water bodies, there is still no definite mode of transmission. Ecological and transmission studies suggest Variable Number Tandem Repeat (VNTR) typing as a useful tool to differentiate MU strains from other Mycolactone Producing Mycobacteria (MPM). Deciphering the genetic relatedness of clinical and environmental isolates is seminal to determining reservoirs, vectors and transmission routes. In this study, we attempted to source-track MU infections to specific water bodies by matching VNTR profiles of MU in human samples to those in the environment. Environmental samples were collected from 10 water bodies in four BU endemic communities in the Ashanti region, Ghana. Four VNTR loci in MU Agy99 genome, were used to genotype environmental MU ecovars, and those from 14 confirmed BU patients within the same study area. Length polymorphism was confirmed with sequencing. MU was present in the 3 different types of water bodies, but significantly higher in biofilm samples. Four MU genotypes, designated W, X, Y and Z, were typed in both human and environmental samples. Other reported genotypes were only found in water bodies. Animal trapping identified 1 mouse with lesion characteristic of BU, which was confirmed as MU infection. Our findings suggest that patients may have been infected from community associated water bodies. Further, we present evidence that small mammals within endemic communities could be susceptible to MU infections. M. ulcerans transmission could involve several routes where humans have contact with risk environments, which may be further compounded by water bodies acting as vehicles for disseminating strains.
| S-EPMC4303273 | biostudies-literature
Project description:BackgroundInvasive bacterial infection (IBI) remains a major burden of mortality and morbidity in children. As coronavirus disease 2019 (COVID-19) emerged, stringent nonpharmaceutical interventions (NPIs) were applied worldwide. This study aimed to evaluate the impact of NPIs on pediatric IBI in Korea.MethodsFrom January 2018 to December 2020, surveillance for pediatric IBIs caused by 9 pathogens (S. pneumoniae, H. influenzae, N. meningitidis, S. agalactiae, S. pyogenes, S. aureus, Salmonella species, L. monocytogenes and E. coli) was performed at 22 hospitals throughout Korea. Annual incidence rates were compared before and after the COVID-19 pandemic.ResultsA total of 651 cases were identified and the annual incidence was 194.0 cases per 100,000 in-patients in 2018, 170.0 in 2019 and 172.4 in 2020. Most common pathogen by age group was S. agalactiae in infants < 3 months (n = 129, 46.7%), S. aureus in 3 to < 24 months (n = 35, 37.2%), Salmonella spp. in 24 to < 60 months (n = 24, 34.8%) and S. aureus in children ≥ 5 years (n = 128, 60.7%). Compared with 2018 to 2019, the incidence rate in 2020 decreased by 57% for invasive pneumococcal disease (26.6 vs. 11.5 per 100,000 in-patients, P = 0.014) and 59% for Salmonella spp. infection (22.8 vs. 9.4 per 100,000 in-patients, P = 0.018). In contrast, no significant changes were observed in invasive infections due to S. aureus, S. agalactiae and E. coli.ConclusionsThe NPIs implemented during the COVID-19 pandemic reduced invasive diseases caused by S. pneumoniae and Salmonella spp. but not S. aureus, S. agalactiae and E. coli in children.
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Project description: Not available
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Project description:IntroductionPathogen spectrum of Hand, foot and mouth disease (HFMD) has substantially changed in the past decade in China. Growing evidence has indicated that anti-COVID-19 nonpharmaceutical interventions (NPIs) can support control of various infectious diseases, including intestinal diseases.MethodsIn this study, HFMD cases were enrolled from sentinel hospitals of Nanchang, Jiangxi province, and enteroviruses were genotyped using specific real time RT-PCR. We systematically characterized the epidemiology of HFMD based on the continuous molecular surveillance and estimated the impact of COVID-19 intervention on HFMD incidence using seasonal autoregressive integrated moving average (ARIMA) models.ResultsA total of 10247 HFMD cases were included during 2010-2022, of which 6121 enterovirus (EV)-positive cases (59.7%) were identified by real-time RT-PCR. Over 80% cases were associated with EV-A71 and coxsackievirus A16 (CVA16) during 2010-2012, while the type distribution significantly changed as CVA6 emerged to be dominant, accounting for 22.6%-59.6% during 2013-2022. It was observed that the prevalence patterns of EV-A71 and CVA16 were similar and both of them peaked in the second quarter and then leveled off. However, CVA6 was generally prevalent around the fourth quarter, demonstrating a staggered prevalence during 2010-2019. During the COVID-19 epidemic, the seasonal HFMD epidemic peak was restrained, and the ARIMA analysis indicated that the COVID-19 intervention had mitigated EV transmission during the first COVID-19 outbreak in early 2020. In addition, bivariate Spearman's cross-correlation coefficients were estimated for the major types CVA6, CVA16 and EV-A71. Our analyses indicated the possible existence of correlations among CVA6, CVA16 and EV-A71 prevalence in the epidemiological level.DiscussionTaken together, the type distribution of HFMD has substantially changed over the last decade and CVA6 and CVA16 are currently the most predominant types co-circulating in Nanchang. The anti-COVID-19 NPIs significantly reduced the incidence of EV infections.
| S-EPMC10618362 | biostudies-literature
Project description:On 12 November 2019, one couple from the Sonid Left Qi (County) in the Inner Mongolia Autonomous Region was diagnosed with pneumonic plague in Beijing. The wife acquired the infection from her husband. Thereafter, two bubonic plague cases were identified in Inner Mongolia on November 16th and 24th. In this study, genome-wide single nucleotide polymorphism (SNP) analysis was used to identify the phylogenetic relationship of Yersinia pestis strains isolated in Inner Mongolia. Strains isolated from reservoirs in 2018 and 2019 in Inner Mongolia, together with the strain isolated from Patient C, were further clustered into 2.MED3m, and two novel lineages (2.MED3q, 2.MED3r) in the 2.MED3 population. According to the analysis of PCR-based molecular subtyping methods, such as the MLVA 14 scheme and seven SNP allele sequencing, Patients A/B and D were classified as 2.MED3m. In addition, strains from rodents living near the patients' residences were clustered into the same lineage as patients. Such observations indicated that human plague cases originated from local reservoirs. Corresponding phylogenetic analysis also indicated that rodent plague strains in different areas in Inner Mongolia belong to different epizootics rather than being caused by spreading from the same epizootic in Meriones unguiculatus in 2019.
| S-EPMC8362994 | biostudies-literature