scholarly journals Phylogenomics reveals multiple introductions and early spread of SARS-CoV-2 into Peru

2020 ◽  
Author(s):  
Eduardo Juscamayta-López ◽  
David Tarazona ◽  
Faviola Valdivia ◽  
Nancy Rojas ◽  
Dennis Carhuaricra ◽  
...  
Keyword(s):  
Mortality Rate ◽  
Severe Acute Respiratory Syndrome ◽  
Genomic Diversity ◽  
Phylogenomic Analysis ◽  
Multiple Introductions ◽  
Transmission Event

ABSTRACTPeru has become one of the countries with the highest mortality rate from the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. To investigate early transmission event and genomic diversity of SARS-CoV-2 isolates circulating in Peru, we analyzed a total of 3472 SARS-CoV-2 genomes, from which 149 ones were from Peru. Phylogenomic analysis revealed multiple and independent introductions of the virus mainly from Europe and Asia. In addition, we found evidence for community-driven transmission of SARS-CoV-2 as suggested by clusters of related viruses found in patients living in different Peru regions.

scholarly journals Do sex-specific immunobiological factors and differences in angiotensin converting enzyme 2 (ACE2) expression explain increased severity and mortality of COVID-19 in males?

Diagnosis ◽  
2020 ◽  
Vol 7 (4) ◽  
pp. 385-386 ◽  
Author(s):  
Jens Vikse ◽  
Giuseppe Lippi ◽  
Brandon Michael Henry
Keyword(s):  
Mortality Rate ◽  
Severe Acute Respiratory Syndrome ◽  
Lung Injury ◽  
Angiotensin Converting Enzyme ◽  
Converting Enzyme ◽  
Sars Coronavirus ◽  
Immunomodulatory Treatment ◽  
Angiotensin Converting Enzyme 2 ◽  
Cytopathic Effects ◽  
Severe Lung

AbstractCoronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2), shares similarities with the former SARS outbreak, which was caused by SARS-CoV-1. SARS was characterized by severe lung injury due to virus-induced cytopathic effects and dysregulated hyperinflammatory state. COVID-19 has a higher mortality rate in men both inside and outside China. In this opinion paper, we describe how sex-specific immunobiological factors and differences in angiotensin converting enzyme 2 (ACE2) expression may explain the increased severity and mortality of COVID-19 in males. We highlight that immunomodulatory treatment must be tailored to the underlying immunobiology at different stages of disease. Moreover, by investigating sex-based immunobiological differences, we may enhance our understanding of COVID-19 pathophysiology and facilitate improved immunomodulatory strategies.

scholarly journals Cerebral venous sinus thrombosis associated with severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) infection

2021 ◽  
pp. 104-104
Author(s):  
Dragan Nikolic ◽  
Marijana Basta-Nikolic ◽  
Vladimir Manojlovic ◽  
Zeljko Zivanovic ◽  
Sanja Vickovic ◽  
...  
Keyword(s):  
Risk Factors ◽  
Mortality Rate ◽  
Severe Acute Respiratory Syndrome ◽  
High Mortality ◽  
Clinical Presentation ◽  
Sinus Thrombosis ◽  
Cerebral Venous Sinus Thrombosis ◽  
Neurological Symptoms ◽  
Venous Sinus ◽  
Venous Sinus Thrombosis

Introduction/Objective. Coagulopathy induced by severe acute respiratory syndrome coronavirus 2 infection (SARS-CoV-2) can be an underlying cause of cerebral venous sinus thrombosis (CVST), a less common type of stroke with a variable clinical presentation and high mortality rate. Objective: to present a series of CVST cases associated with SARS-CoV-2 infection. Methods. This retrospective study evaluated clinical, laboratory and radiological presentation, risk factors, barriers to diagnosis, treatment and outcome of patients with SARS-CoV-2 infection induced CVST. Results. The study comprised 6 patients diagnosed with COVID-19 induced CVST during the 18 months period. Majority (66.7%) had no significant risk factors for developing CVST. Median time from initial COVID-19 diagnosis to onset of neurologic deficit was 7 days (interquartile range 0.5-7 days). Clinical presentation comprised non specific neurological symptoms: headache (83.3%) and decreased consciousness (33.3%), together with elevated levels of D-dimer and inflammatory biomarkers. The transverse (n = 4 or 66.7%), superior sagittal sinuses (n = 3 or 50%) and sigmoid sinus (n = 2 or 33.3%) were most commonly affected. Five patients (83.3%) had minimal to no symptoms at discharge (mRS ? 2). In-hospital mortality in our current series was relatively high (16.7%). Conclusion. The high mortality rate of SARS-CoV-2-associated CVST urges clinicians to suspect CVST in patients with a history of COVID-19 infection presenting with non-specific neurological symptoms in order to provide proper treatment and prevent complications.

scholarly journals Effect of Convalescent Plasma Therapy on Viral Shedding and Survival in Patients With Coronavirus Disease 2019

2020 ◽  
Vol 222 (1) ◽  
pp. 38-43 ◽  
Author(s):  
Qing-Lei Zeng ◽  
Zu-Jiang Yu ◽  
Jian-Jun Gou ◽  
Guang-Ming Li ◽  
Shu-Huan Ma ◽  
...  
Keyword(s):  
Respiratory Failure ◽  
Mortality Rate ◽  
Severe Acute Respiratory Syndrome ◽  
Plasma Treatment ◽  
Critically Ill Patients ◽  
Plasma Therapy ◽  
Viral Shedding ◽  
Almost All ◽  
End Stage

Abstract Currently, coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been reported in almost all countries globally. No effective therapy has been documented for COVID-19, and the role of convalescent plasma therapy is unknown. In the current study, 6 patients with COVID-19 and respiratory failure received convalescent plasma a median of 21.5 days after viral shedding was first detected, all tested negative for SARS-CoV-2 RNA within 3 days after infusion, and 5 eventually died. In conclusion, convalescent plasma treatment can end SARS-CoV-2 shedding but cannot reduce the mortality rate in critically ill patients with end-stage COVID-19, and treatment should be initiated earlier.

scholarly journals COVID-19: A positive prospect of pandemic situation

2021 ◽  
Vol 58 (1) ◽  
pp. 2912-2914
Author(s):  
Vinod Kumar Et al.
Keyword(s):  
Air Pollution ◽  
Mortality Rate ◽  
Severe Acute Respiratory Syndrome ◽  
East Asian ◽  
Preventive Measure ◽  
Human Race ◽  
Wuhan City ◽  
Significant Drop ◽  
The World ◽  
Short Span

In 2019, human race again came across a highly transmittable and pathogenic viral infection viz. COVID-19 and along with its pandemic nature, caused severe acute respiratory syndrome (SARS), and owes its emergence from the local seafood market of Wuhan city, China. Corona virus is currently prevalent all over the world wherein it caused infection in more than 1,30,000 individuals worldwide with mortality rate nearby 3% in approximately 120 countries within a short span of time and the infection due to this virus is still on a higher verge. Apart from this as per WHO report on air pollution revealed around 2.4 and 2.2 million deaths in South East Asian and Western Pacific regions respectively. Both conditions are deadly in their respective prospects, although lockdown, preventive measure which avoid spreading of COVID-19 infection, indirectly lead to significant drop down in air pollution globally. However, this effect is not permanent and it is for being a time but it develops a hope that together we can fight against both.

scholarly journals Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)

2017 ◽  
Author(s):  
Matthew Parks ◽  
Teofil Nakov ◽  
Elizabeth Ruck ◽  
Norman J. Wickett ◽  
Andrew J. Alverson
Keyword(s):  
Whole Genome Duplication ◽  
Large Scale ◽  
Genome Duplication ◽  
Gene Tree ◽  
Genomic Diversity ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
Gene Trees ◽  
Angiosperm Evolution ◽  
Polyploid Formation

ABSTRACTPremise of the studyDiatoms are one of the most species-rich lineages of microbial eukaryotes. Similarities in clade age, species richness, and contributions to primary production motivate comparisons to flowering plants, whose genomes have been inordinately shaped by whole genome duplication (WGD). These events that have been linked to speciation and increased rates of lineage diversification, identifying WGDs as a principal driver of angiosperm evolution. We synthesized a relatively large but scattered body of evidence that, taken together, suggests that polyploidy may be common in diatoms.MethodsWe used data from gene counts, gene trees, and patterns of synonymous divergence to carry out the first large-scale phylogenomic analysis of genome-scale duplication histories for a phylogenetically diverse set of 37 diatom taxa.Key resultsSeveral methods identified WGD events of varying age across diatoms, though determining the exact number and placement of events and, more broadly, inferences of WGD at all, were greatly impacted by gene-tree uncertainty. Gene-tree reconciliations supported allopolyploidy as the predominant mode of polyploid formation, with particularly strong evidence for ancient allopolyploid events in the thalassiosiroid and pennate diatom clades.ConclusionsWhole genome duplication appears to have been an important driver of genome evolution in diatoms. Denser taxon sampling will better pinpoint the timing of WGDs and likely reveal many more of them. We outline potential challenges in reconstructing paleopolyploid events in diatoms that, together with these results, offer a framework for understanding the evolutionary roles of genome duplication in a group that likely harbors substantial genomic diversity.

scholarly journals Comparative genomics confirms a rare melioidosis human-to-human transmission event and reveals incorrect phylogenomic reconstruction due to polyclonality

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
Ammar Aziz ◽  
Bart J. Currie ◽  
Mark Mayo ◽  
Derek S. Sarovich ◽  
Erin P. Price
Keyword(s):  
Primary Culture ◽  
Type Species ◽  
Sputum Sample ◽  
Phylogenomic Analysis ◽  
Content Type ◽  
Transmission Event ◽  
Bioinformatic Tools ◽  
Link Type ◽  
Sequence Types ◽  
Polyclonal Infection

Human-to-human transmission of the melioidosis bacterium, Burkholderia pseudomallei , is exceedingly rare, with only a handful of suspected cases documented to date. Here, we used whole-genome sequencing (WGS) to characterize one such unusual B. pseudomallei transmission event, which occurred between a breastfeeding mother with mastitis and her child. Two strains corresponding to multilocus sequence types (STs)-259 and -261 were identified in the mother’s sputum from both the primary culture sweep and in purified colonies, confirming an unusual polyclonal infection in this patient. In contrast, primary culture sweeps of the mother’s breast milk and the child’s cerebrospinal fluid and blood samples contained only ST-259, indicating monoclonal transmission to the child. Analysis of purified ST-259 isolates showed no genetic variation between mother and baby isolates, providing the strongest possible evidence of B. pseudomallei human-to-human transmission, probably via breastfeeding. Next, phylogenomic analysis of all isolates, including the mother’s mixed ST-259/ST-261 sputum sample, was performed to investigate the effects of mixtures on phylogenetic inference. Inclusion of this mixture caused a dramatic reduction in the number of informative SNPs, resulting in branch collapse of ST-259 and ST-261 isolates, and several instances of incorrect topology in a global B. pseudomallei phylogeny, resulting in phylogenetic incongruence. Although phylogenomics can provide clues about the presence of mixtures within WGS datasets, our results demonstrate that this methodology can lead to phylogenetic misinterpretation if mixed genomes are not correctly identified and omitted. Using current bioinformatic tools, we demonstrate a robust method for bacterial mixture identification and strain parsing that avoids these pitfalls.

scholarly journals Genomic Insights of Multidrug-Resistant Escherichia coli From Wastewater Sources and Their Association With Clinical Pathogens in South Africa

2021 ◽  
Vol 8 ◽  
Author(s):  
Joshua Mbanga ◽  
Daniel G. Amoako ◽  
Akebe L. K. Abia ◽  
Mushal Allam ◽  
Arshad Ismail ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Virulence Genes ◽  
Treatment Plant ◽  
Multidrug Resistant ◽  
Genomic Diversity ◽  
Health Concern ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
E Coli ◽  
Wwtp Effluent

There is limited information on the comparative genomic diversity of antibiotic-resistant Escherichia coli from wastewater. We sought to characterize environmental E. coli isolates belonging to various pathotypes obtained from a wastewater treatment plant (WWTP) and its receiving waters using whole-genome sequencing (WGS) and an array of bioinformatics tools to elucidate the resistomes, virulomes, mobilomes, clonality, and phylogenies. Twelve multidrug-resistant (MDR) diarrheagenic E. coli isolates were obtained from the final effluent of a WWTP, and the receiving river upstream and downstream of the WWTP were sequenced on an Illumina MiSeq machine. The multilocus sequence typing (MLST) analysis revealed that multiple sequence types (STs), the most common of which was ST69 (n = 4) and ST10 (n = 2), followed by singletons belonging to ST372, ST101, ST569, ST218, and ST200. One isolate was assigned to a novel ST ST11351. A total of 66.7% isolates were positive for β-lactamase genes with 58.3% harboring the blaTEM1B gene and a single isolate the blaCTX−M−14 and blaCTX−M−55 extended-spectrum β-lactamase (ESBL) genes. One isolate was positive for the mcr-9 mobilized colistin resistance gene. Most antibiotic resistance genes (ARGs) were associated with mobile genetic support: class 1 integrons (In22, In54, In191, and In369), insertion sequences (ISs), and/or transposons (Tn402 or Tn21). A total of 31 virulence genes were identified across the study isolates, including those responsible for adhesion (lpfA, iha, and aggR), immunity (air, gad, and iss), and toxins (senB, vat, astA, and sat). The virulence genes were mostly associated with IS (IS1, IS3, IS91, IS66, IS630, and IS481) or prophages. Co-resistance to heavy metal/biocide, antibiotics were evident in several isolates. The phylogenomic analysis with South African E. coli isolates from different sources (animals, birds, and humans) revealed that isolates from this study mostly clustered with clinical isolates. Phylogenetics linked with metadata revealed that isolates did not cluster according to source but according to ST. The occurrence of pathogenic and MDR isolates in the WWTP effluent and the associated river is a public health concern.

scholarly journals The first two months of COVID-19 pandemic in Bosnia and Herzegovina: Single-center experience

2020 ◽  
Author(s):  
Jurica Arapović ◽  
Siniša Skočibušić
Keyword(s):  
Mortality Rate ◽  
Severe Acute Respiratory Syndrome ◽  
Bosnia And Herzegovina ◽  
The Novel ◽  
Single Center ◽  
Single Centre ◽  
Single Center Experience ◽  
Single Centre Experience ◽  
Novel Coronavirus ◽  
The University

The novel coronavirus disease 2019 (COVID-19) pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is still progressing and has been recorded in more than 210 countries and territories worldwide. In Bosnia and Herzegovina, the first cases of COVID-19 were detected on 5th of March 2020 in the entity of Republic of Srpska and 9th of March 2020 in the entity of Federation of Bosnia and Herzegovina. Up until the 16th of May 2020, more than 2,200 COVID-19 cases were recorded in both entities, with a mortality rate of 5.8% (131 out of 2231 cases). The aim of this ongoing study is to present the current epidemiological and sociodemographic parameters of 380 COVID-19 patients diagnosed at the University Clinical Hospital Mostar (UCH Mostar) during the first two months of the COVID-19 pandemic. Out of 380 patients, 60 (15.8%) of them required hospitalization. The mortality rate was 5% (19/380). The highest mortality rate of 15.2% (12/79) was recorded in the patients age ≥65 years. In addition to this single-centre experience of the ongoing COVID-19 pandemic, we discuss the epidemiological measures imposed in Bosnia and Herzegovina, with emphasis on the restrictive ones. The COVID-19 pandemic is still ongoing in Bosnia and Herzegovina.

scholarly journals Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism

mBio ◽  
2019 ◽  
Vol 10 (2) ◽  
Author(s):  
Disa Bäckström ◽  
Natalya Yutin ◽  
Steffen L. Jørgensen ◽  
Jennah Dharamshi ◽  
Felix Homa ◽  
...  
Keyword(s):  
Deep Sea ◽  
Genomic Diversity ◽  
Genome Comparison ◽  
Phylogenomic Analysis ◽  
Dna Viruses ◽  
Deep Sea Sediments ◽  
Giant Viruses ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Loki’S Castle ◽  
Virus Genomes

ABSTRACT The nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes (proposed order, “Megavirales”) include the families Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Phycodnaviridae, Marseilleviridae, and Mimiviridae, as well as still unclassified pithoviruses, pandoraviruses, molliviruses, and faustoviruses. Several of these virus groups include giant viruses, with genome and particle sizes exceeding those of many bacterial and archaeal cells. We explored the diversity of the NCLDV in deep sea sediments from the Loki’s Castle hydrothermal vent area. Using metagenomics, we reconstructed 23 high-quality genomic bins of novel NCLDV, 15 of which are related to pithoviruses, 5 to marseilleviruses, 1 to iridoviruses, and 2 to klosneuviruses. Some of the identified pithovirus-like and marseillevirus-like genomes belong to deep branches in the phylogenetic tree of core NCLDV genes, substantially expanding the diversity and phylogenetic depth of the respective groups. The discovered viruses, including putative giant members of the family Marseilleviridae, have a broad range of apparent genome sizes, in agreement with the multiple, independent origins of gigantism in different branches of the NCLDV. Phylogenomic analysis reaffirms the monophyly of the pithovirus-iridovirus-marseillevirus branch of the NCLDV. Similarly to other giant viruses, the pithovirus-like viruses from Loki’s Castle encode translation systems components. Phylogenetic analysis of these genes indicates a greater bacterial contribution than had been detected previously. Genome comparison suggests extensive gene exchange between members of the pithovirus-like viruses and Mimiviridae. Further exploration of the genomic diversity of Megavirales in additional sediment samples is expected to yield new insights into the evolution of giant viruses and the composition of the ocean megavirome. IMPORTANCE Genomics and evolution of giant viruses are two of the most vigorously developing areas of virus research. Lately, metagenomics has become the main source of new virus genomes. Here we describe a metagenomic analysis of the genomes of large and giant viruses from deep sea sediments. The assembled new virus genomes substantially expand the known diversity of the nucleocytoplasmic large DNA viruses of eukaryotes. The results support the concept of independent evolution of giant viruses from smaller ancestors in different virus branches.

Revisiting the antiviral efficacy of terpenoids: Plausible adjunct therapeutics for novel SARS-CoV-2?

2021 ◽  
Vol 21 ◽  
Author(s):  
Afza Ahmad ◽  
Rohit Kumar Tiwari ◽  
Irfan Ahmad Ansari
Keyword(s):  
Mortality Rate ◽  
Severe Acute Respiratory Syndrome ◽  
Scientific Literature ◽  
Bioactive Constituents ◽  
Plant Metabolites ◽  
Secondary Plant Metabolites ◽  
Chemical Structures ◽  
Antiviral Efficacy ◽  
The World ◽  
History Of

: Presently the world is witnessing most devastating pandemic in the history of mankind caused due to Severe Acute Respiratory Syndrome or SARS-CoV-2. This dreaded pandemic is responsible for escalated mortality rate across the globe and thus is the worst catastrophes in the history of mankind. Since its outbreak, substantial scientific explorations focusing on formulation of novel therapeutical and/or adjunct intervention against the disease are continuously in pipeline. However, till date no effective therapy has been approved and hence the present alarming situation urges the necessity of exploring novel, safe and efficient interventional strategies. Functionally, terpenoids are a class of secondary plant metabolites having multi facet chemical structures and are categorically documented to be the largest reservoir of bioactive constituents, predominant in nature. Intriguingly, very little is scientifically explored or reviewed in regards with the anti-CoV-2 attributes of terpenoids. The present article thus aims to revisit the antiviral efficacy of terpenoids by reviewing the current scientific literature and thereby provide an opinion on the plausibility of exploring them as potential therapeutical intervention to deal with ongoing CoV-2 pandemic.

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