Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
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Venezuela and Colombia both adopted measures of containment early in response to the COVID-19 pandemic. However, Venezuela's ongoing humanitarian crisis has decimated its health care system, and forced millions of Venezuelans to flee through its porous border with Colombia. The extensive shared border, and illegal cross-border transit through improvised trails between the two countries are major challenges for public health authorities. We report the first SARS-CoV-2 genomes from Venezuela, and present a snapshot of the SARS-CoV-2 epidemiologic landscape in the Colombian-Venezuelan border region. ⋯ Genomic sequencing demonstrates similarity between SARS-CoV-2 lineages from Venezuela and viruses collected from patients in bordering areas in Colombia and from Brazil, consistent with cross-border transit despite administrative measures including lockdowns. The presence of mutations associated with increased infectivity in the 3 Venezuelan genomes we report and Colombian SARS-CoV-2 genomes from neighboring borders areas may pose additional challenges for control of SARS-CoV-2 spread in the complex epidemiological landscape in Latin American countries. Public health authorities should carefully follow the progress of the pandemic and its impact on displaced populations within the region.
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Infect. Genet. Evol. · Nov 2020
Quasi-species nature and differential gene expression of severe acute respiratory syndrome coronavirus 2 and phylogenetic analysis of a novel Iranian strain.
A novel coronavirus related to severe acute respiratory syndrome virus, (SARS-CoV-2) is the causal agent of the COVID-19 pandemic. Despite the genetic mutations across the SARS-CoV-2 genome being recently investigated, its transcriptomic genetic polymorphisms at inter-host level and the viral gene expression level based on each Open Reading Frame (ORF) remains unclear. Using available High Throughput Sequencing (HTS) data and based on SARS-CoV-2 infected human transcriptomic data, this study presents a high-resolution map of SARS-CoV-2 single nucleotide polymorphism (SNP) hotspots in a viral population at inter-host level. ⋯ Ancestor analysis of the isolates from different locations including Iran suggest shared Chinese ancestry. These results propose the importance of potential inter-host level genetic variations to the evolution of SARS-COV-2, and the formation of viral quasi-species. The RNA modifications discovered in this study may cause amino acid sequence changes in polyprotein, spike protein, product of ORF8 and nucleocapsid (N) protein, suggesting further insights to understanding the functional impacts of mutations in the life cycle and pathogenicity of SARS-CoV-2.
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Infect. Genet. Evol. · Nov 2020
Comparative Study Observational StudyDifferences of inflammatory and non-inflammatory indicators in Coronavirus disease-19 (COVID-19) with different severity.
Background A variety of inflammatory and non-inflammatory indicators were increased in severe and critical Coronavirus disease-19 (COVID-19) and some of them were used to evaluate the severity and predict prognosis of community-acquired pneumonia. The aim of this study was to investigate the association of these indicators in COVID-19 with different severity. Methods Clinical data of 46 patients with severe COVID-19 and 31 patients with critical COVID-19 were collected. ⋯ Conclusions The severe and critical COVID-19 patients had significant differences in concentrations of serum cTnI, D-D, CRP, IL-6, PCT, neutrophil and lymphocyte counts. The increase of cTnI, CRP, IL-6, PCT, neutrophils and decrease of lymphocytes indicated severe condition. The initial IL-6 might be a good indicator of COVID-19 severity.
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Infect. Genet. Evol. · Oct 2020
Identification of potential inhibitors against SARS-CoV-2 by targeting proteins responsible for envelope formation and virion assembly using docking based virtual screening, and pharmacokinetics approaches.
WHO has declared the outbreak of COVID-19 as a public health emergency of international concern. The ever-growing new cases have called for an urgent emergency for specific anti-COVID-19 drugs. Three structural proteins (Membrane, Envelope and Nucleocapsid protein) play an essential role in the assembly and formation of the infectious virion particles. ⋯ Caffeic acid and ferulic acid were found to inhibit SARS-CoV-2 membrane protein while the anti-viral agent's simeprevir and grazoprevir showed a high binding affinity for nucleocapsid protein. All these compounds not only showed excellent pharmacokinetic properties, absorption, metabolism, minimal toxicity and bioavailability but were also remain stabilized at the active site of proteins during the MD simulation. Thus, the identified lead compounds may act as potential molecules for the development of effective drugs against SARS-CoV-2 by inhibiting the envelope formation, virion assembly and viral pathogenesis.
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Infect. Genet. Evol. · Oct 2020
Meta AnalysisAssociation between ABO blood groups and COVID-19 infection, severity and demise: A systematic review and meta-analysis.
The COVID-19 spreads rapidly around the world which has brought a global health crisis. The pathogen of COVID-19 is SARS-COV-2, and previous studies have proposed the relationship between ABO blood group and coronavirus. Here, we aim to delve into the association between ABO blood group and COVID-19 infection, severity and demise. ⋯ The current meta-analysis suggest that blood type A might be more susceptible to infect COVID-19 while blood type O might be less susceptible to infect COVID-19; there were no correlation between ABO blood group and severity or demise of COVID-19. However, more investigation and research are warranted to clarify the relationship between COVID-19 and ABO blood type.