scholarly journals Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 184
Author(s):  
Alejandro Flores-Alanis ◽  
Armando Cruz-Rangel ◽  
Flor Rodríguez-Gómez ◽  
James González ◽  
Carlos Alberto Torres-Guerrero ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Spike Protein ◽  
The Novel ◽  
Molecular Surveillance ◽  
Low Genetic Diversity ◽  
Geographical Regions ◽  
Frequent Mutations ◽  
One Year ◽  
The City ◽  
Over Time

In December 2019, the first cases of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified in the city of Wuhan, China. Since then, it has spread worldwide with new mutations being reported. The aim of the present study was to monitor the changes in genetic diversity and track non-synonymous substitutions (dN) that could be implicated in the fitness of SARS-CoV-2 and its spread in different regions between December 2019 and November 2020. We analyzed 2213 complete genomes from six geographical regions worldwide, which were downloaded from GenBank and GISAID databases. Although SARS-CoV-2 presented low genetic diversity, there has been an increase over time, with the presence of several hotspot mutations throughout its genome. We identified seven frequent mutations that resulted in dN substitutions. Two of them, C14408T>P323L and A23403G>D614G, located in the nsp12 and Spike protein, respectively, emerged early in the pandemic and showed a considerable increase in frequency over time. Two other mutations, A1163T>I120F in nsp2 and G22992A>S477N in the Spike protein, emerged recently and have spread in Oceania and Europe. There were associations of P323L, D614G, R203K and G204R substitutions with disease severity. Continuous molecular surveillance of SARS-CoV-2 will be necessary to detect and describe the transmission dynamics of new variants of the virus with clinical relevance. This information is important to improve programs to control the virus.

scholarly journals Molecular Epidemiology Surveillance of SARS-Cov-2: Mutations and Genetic Diversity One Year After Emerging

2021 ◽  
Author(s):  
Alejandro Flores-Alanis ◽  
Armando Cruz-Rangel ◽  
Flor Rodríguez-Gómez ◽  
James González ◽  
Carlos Alberto Torres-Guerrero ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genomic Analysis ◽  
Viral Fitness ◽  
Spike Protein ◽  
Molecular Surveillance ◽  
Low Genetic Diversity ◽  
Geographical Regions ◽  
Frequent Mutations ◽  
One Year ◽  
Over Time

In December 2019, the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the province of Wuhan, China. Since then, it has spread worldwide with new mutations being reported. We performed genomic analysis to identify the changes in genetic diversity of SARS-CoV-2 between December 2019 and November 2020, and through molecular surveillance, we monitored the mutations that could be involved in viral fitness. We analyzed 2,213 complete genomes from 6 geographical regions worldwide, which were downloaded from GenBank and GISAID databases. Although SARS-CoV-2 presented low genetic diversity, there has been an increase over time, with the presence of several hotspot mutations throughout its genome. We identified 7 frequent mutations that resulted in non-synonymous substitutions (dN). Two of them, C14408T>P323L and A23403G>D614G, located in the nsp12 and Spike protein, respectively, emerged early in the pandemic and showed a considerable increase in frequency over time. Two other mutations, A1163T>I120F in nsp2 and G22992A>S477N in the Spike protein emerged recently and have spread in Oceania and Europe. Continuous molecular surveillance of SARS-CoV-2 will be necessary to detect and describe the transmission dynamics of new variants of the virus with clinical relevance. This information is important to improve programs to control the virus.

L’absence chez Michel Butor. L’Emploi du temps et Degrés

2012 ◽  
pp. 66-80
Author(s):  
Michał Mrozowicki
Keyword(s):  
Human Memory ◽  
Point Of View ◽  
Narrative Discourse ◽  
The Novel ◽  
Michel Butor ◽  
Starting Point ◽  
One Year ◽  
The Moment ◽  
Narrative Mode ◽  
The City

Michel Butor, born in 1926, one of the leaders of the French New Novel movement, has written only four novels between 1954 and 1960. The most famous of them is La Modification (Second thoughts), published in 1957. The author of the paper analyzes two other Butor’s novels: L’Emploi du temps (Passing time) – 1956, and Degrés (Degrees) – 1960. The theme of absence is crucial in both of them. In the former, the novel, presented as the diary of Jacques Revel, a young Frenchman spending a year in Bleston (a fictitious English city vaguely similar to Manchester), describes the narrator’s struggle to survive in a double – spatial and temporal – labyrinth. The first of them, formed by Bleston’s streets, squares and parks, is symbolized by the City plan. During his one year sojourn in the city, using its plan, Revel learns patiently how to move in its different districts, and in its strange labyrinth – strange because devoid any centre – that at the end stops annoying him. The other, the temporal one, symbolized by the diary itself, the labyrinth of the human memory, discovered by the narrator rather lately, somewhere in the middle of the year passed in Bleston, becomes, by contrast, more and more dense and complex, which is reflected by an increasinly complex narration used to describe the past. However, at the moment Revel is leaving the city, he is still unable to recall and to describe the events of the 29th of February 1952. This gap, this absence, symbolizes his defeat as the narrator, and, in the same time, the human memory’s limits. In Degrees temporal and spatial structures are also very important. This time round, however, the problems of the narration itself, become predominant. Considered from this point of view, the novel announces Gerard Genette’s work Narrative Discourse and his theoretical discussion of two narratological categories: narrative voice and narrative mode. Having transgressed his narrative competences, Pierre Vernier, the narrator of the first and the second parts of the novel, who, taking as a starting point, a complete account of one hour at school, tries to describe the whole world and various aspects of the human civilization for the benefit of his nephew, Pierre Eller, must fail and disappear, as the narrator, from the third part, which is narrated by another narrator, less audacious and more credible.

Genome typing and epidemiology of human listeriosis in New Zealand 1999-2018

2021 ◽  
Author(s):  
Lucia Rivas ◽  
Shevaun Paine ◽  
Pierre-Yves Dupont ◽  
Audrey Tiong ◽  
Beverley Horn ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
New Zealand ◽  
Epidemiological Data ◽  
Common Source ◽  
Snp Analysis ◽  
Whole Genome ◽  
Single Nucleotide ◽  
Low Genetic Diversity ◽  
Geographical Regions ◽  
Sequence Types

This study describes the epidemiology of listeriosis in New Zealand (NZ) between 1999 and 2018, as well as the retrospective whole genome sequencing (WGS) of 453 Listeria monocytogenes isolates corresponding to 95% of the human cases within this period. The average notified rate of listeriosis was 0.5 cases per 100,000 population and non-pregnancy associated cases were more prevalent than pregnancy-associated cases (average 19 and 5 cases per annum, respectively). Analysis of WGS data was assessed using multi-locus sequencing typing (MLST), including core-genome and whole-genome MLST (cgMLST and wgMLST) and single-nucleotide polymorphism (SNP) analysis. Thirty-nine sequence types (STs) were identified, with the most common being, ST1 (21.9%), ST4 (13.2%), ST2 (11.3%), ST120 (6.1%) and ST155 (6.4%). A total of 291 different cgMLST types were identified, with the majority (n = 243) of types observed as a single isolate, consistent with the observation that listeriosis is predominately sporadic. Amongst the 49 cgMLST types containing two or more isolates, 18 cgMLST types contained 2-4 isolates (50 isolates in total, including three outbreak-associated isolates) that shared low genetic diversity (0-2 whole-genome alleles), some of which were dispersed in time or geographical regions. SNP-analysis also produced comparable results to wgMLST. The low genetic diversity within these clusters suggests a potential common source but incomplete epidemiological data impaired retrospective epidemiological investigations. Prospective use of WGS analysis, together with thorough exposure information from cases will potentially identify future outbreaks more rapidly and possibly those that have been undetected for some time over different geographically regions.

‘These Acres of Print’: Charles Dickens, the News and the Novel as Pattern

2020 ◽  
pp. 26-58
Author(s):  
Jessica R. Valdez
Keyword(s):  
Charles Dickens ◽  
The Novel ◽  
Reading Public ◽  
Serial Output ◽  
Benedict Anderson ◽  
Serial Publication ◽  
City Of London ◽  
The City ◽  
Serial Fiction ◽  
Over Time

While Benedict Anderson has argued that newspapers enable readers to imagine national community, Charles Dickens’s writings are attentive to the varying ways that the newspaper press might shape, inhibit, or fragment community through its uncontrolled production of miscellaneous content and matter. This first chapter shows the growing distinction that Dickens drew between fiction and nonfiction, novel and newspaper, in his communal visions for serial publication. Early Dickens characterised the newspaper press as a meteorological force of destruction, a thunderstorm threatening to engulf the city of London, yet continually produced to meet the endless public appetite for more news. Over the course of his career, Dickens experimented with other metaphors for the working of serial narrative and its influence on a reading public. From an intangible creature telling stories to a weaver at his loom, Dickens encourages readers to see the instance of a particular serial output linked to its larger structure over time. In doing so, he privileges the power of serial fiction to cultivate new ways of envisioning community.

scholarly journals Conservation analysis and screening of Ayurvedic compounds against SARS-CoV-2 Spike protein

2020 ◽  
Author(s):  
Zarrin Basharat ◽  
Muhammad Jahanzaib ◽  
Noor Rahman ◽  
Ishtiaq Ahmad Khan ◽  
Azra Yasmin
Keyword(s):  
Caspase 3 ◽  
Spike Protein ◽  
The Novel ◽  
Post Translational Modification ◽  
S Protein ◽  
Conservation Analysis ◽  
The Past ◽  
Online Tools ◽  
Novel Coronavirus ◽  
Over Time

Abstract Recent infections caused by the novel coronavirus (SARS-CoV-2) have led to global panic and mortality. Here, we analyzed the spike (S) protein of this virus using bioinformatics tools. We aimed to determine relative changes among different coronavirus species over the past two decades and to understand the conservation of the S-protein. Representative sequences of coronaviruses were collected from humans and other animals between 2000 and 2020. Evolutionary analyses found that the S-protein did not evolve overnight, but rather continuously over time. Post-translational modification (PTM) analysis using online tools and virtual screening of S-protein against a phytochemical database of Ayurvedic medicinal compounds (n = 2103) identified the S-protein inhibitors. Among these, top ranked were Gingerol (IUPAC name: 4'-Me ether, 3,5-di-Ac 3,5-di-Gingerdiols), 1-(5-Butyltetrahydro-2-furanyl)-2-hexacosanone and Ginsenoyne N ginseng that stimulates Caspase-3, Caspase-8, and the immune system. Gingerol is found in the fresh ginger and has reputation of being a potent antiviral. These compounds might prove useful to design drugs against COVID-19.

Genetic consequences of long-term isolation for the last French population of Eryngium viviparum (Apiaceae)

2019 ◽  
Vol 191 (2) ◽  
pp. 285-298 ◽  
Author(s):  
Pauline Rascle ◽  
Elodie Flaven ◽  
Frédéric Bioret ◽  
Sylvie Magnanon ◽  
Erwan Glemarec ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Conservation Status ◽  
Disjunct Distribution ◽  
French Population ◽  
Endemic Plant ◽  
Evolutionary Potential ◽  
The North ◽  
Low Genetic Diversity ◽  
Geographical Regions ◽  
Seasonally Flooded

Abstract Eryngium viviparum (Apiaceae) is an endangered endemic plant of the Atlantic region of Europe, growing in seasonally flooded sites, and is characterized by a highly disjunct distribution. It occurs in just a few sites in the north-western part of the Iberian Peninsula and in a single locality in France. To improve the conservation status of E. viviparum in France, a conservation programme has been implemented to reintroduce the species. Before considering such an operation, genetic studies were conducted to determine the genetic status of the last French population and to identify the genetic source that should be considered for the best reintroduction strategy. Using microsatellite markers, we documented the genetic structure of the last French population and compared its genetic diversity with that of ten Iberian populations, which cover the three geographical regions where the species occurs. As expected, the French population of E. viviparum shows low genetic diversity due to a bottleneck and geographical isolation. The evolutionary potential appears low, with no private alleles in this population. Furthermore, this population is highly differentiated from the Iberian populations in terms of genetic variation and ecological niche. These results bring new questions regarding the conservation of E. viviparum in France, especially for management and reintroduction aimed at favouring genetic diversity and avoiding extinction.

scholarly journals Surveillance of genetic diversity and evolution in locally transmitted SARS-CoV-2 in Pakistan during the first wave of the COVID-19 pandemic

2021 ◽  
Author(s):  
Muhammad Shakeel ◽  
Muhammad Irfan ◽  
Zaibunnisa ◽  
Muhammad Rashid ◽  
Sabeeta Kanwal Ansari ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Hot Spot ◽  
Spike Protein ◽  
Independent Events ◽  
Recurrent Mutations ◽  
The Usa ◽  
Spatio Temporal ◽  
B Lineage ◽  
The Uk ◽  
The City

AbstractSurveillance of genetic diversity in the SARS-CoV-2 is extremely important to detect the emergence of more infectious and deadly strains of the virus. In this study, we monitored mutational events in the SARS-CoV-2 genome through whole genome sequencing. The samples (n=48) were collected from the hot spot regions of the metropolitan city Karachi, Pakistan during the four months (May 2020 to August 2020) of first wave of the COVID-19 pandemic. The data analysis highlighted 122 mutations, including 120 single nucleotide variations (SNV), and 2 deletions. Among the 122 mutations, there were 71 singletons, and 51 recurrent mutations. A total of 16 mutations, including 5 nonsynonymous mutations, were detected in spike protein. Notably, the spike protein missense mutation D614G was observed in 31 genomes. The phylogenetic analysis revealed majority of the genomes (36) classified as B lineage, where 2 genomes were from B.6 lineage, 5 genomes from B.1 ancestral lineage and remaining from B.1 sub-lineages. It was noteworthy that three clusters of B.1 sub-lineages were observed, including B.1.36 lineage (10 genomes), B.1.160 lineage (11 genomes), and B.1.255 lineage (5 genomes), which represent independent events of SARS-CoV-2 transmission within the city. The sub-lineage B.1.36 had higher representation from the Asian countries and the UK, B.1.160 correspond to the European countries with highest representation from the UK, Denmark, and lesser representation from India, Saudi Arabia, France and Switzerland, and the third sub-lineage (B.1.255) correspond to the USA. Collectively, our study provides meaningful insight into the evolution of SARS-CoV-2 lineages in spatio-temporal local transmission during the first wave of the pandemic.

Genetic Diversity Within and Among Populations of Shorea Robusta Roxb. Ex Gaertn. In Bangladesh and Its Implications for Conservation

2021 ◽  
Vol 50 (2) ◽  
pp. 405-412
Author(s):  
Pragga Saha Sharmi ◽  
Md Abul Kashem ◽  
Rifat Samad ◽  
Mohammad Zabed Hossain
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Isolation By Distance ◽  
Genetic Erosion ◽  
Mantel Test ◽  
Small Population ◽  
Deciduous Forests ◽  
Shorea Robusta ◽  
Low Genetic Diversity ◽  
Geographical Regions

Fragmentation and reduction of natural population size render threats to the conservation of forest resources through depletion of genetic diversity. Hence, information on genetic structure of Sal (Shorea robusta Roxb. ex Gaertn.) populations is relevant for proper management and conservation of the tropical deciduous forests. The present study focused on assessing the genetic diversity of the populations of Sal which was the dominant tree species of the deciduous forests of Bangladesh. Plant leaf samples were collected from the three populations of Sal distributed in the three geographical regions including Madhupur tract in the districts Tangail and Gazipur and that of the districts of Cumilla and Dinajpur. DNA band profiles were generated using eight ISSR primers for a total of 13 samples taken from the three populations. Statistical analysis was done using PopGen 32 and GenAlEx 6.5 softwares. Principal coordinate analysis done on the DNA band profiles revealed that Sal populations of Madhupur tract and Cumilla positioned nearby while Dinajpur showed maximum genetic distance with that of Cumilla. Mantel test showed significant (p=0.05) correlation between genetic and geographic distances indicating “Isolation by Distance”. Data of the present study indicated higher genetic polymorphism (68.87%) in the Sal population of Madhupur tract compared to other two populations. Small population size of Sal of Dinajpur forest might be related with its low genetic diversity. Data of the present study suggest immediate attention for the conservation of Sal forests in Bangladesh before further genetic erosion occurs. Bangladesh J. Bot. 50(2): 405-412, 2021 (June)

scholarly journals Plasmodium falciparum Genetic Diversity in Panamá Based on glurp, msp-1 and msp-2 Genes: Implications for Malaria Elimination in Mesoamerica

Life ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 319
Author(s):  
Ana María Santamaría ◽  
Vanessa Vásquez ◽  
Chystrie Rigg ◽  
Dianik Moreno ◽  
Luis Romero ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Malaria Elimination ◽  
Multiple Correspondence Analysis ◽  
Strong Association ◽  
Parasite Load ◽  
Molecular Surveillance ◽  
Disease Propagation ◽  
Low Genetic Diversity ◽  
Imported Cases ◽  
Endemic Areas

Panamá, together with all the nations in Mesoamerica, has committed to eliminate malaria from the region by 2020. As these countries approach malaria elimination and local transmission decreases, an active molecular surveillance to identify genotypes circulating along the border areas is particularly needed to accurately infer infection origin, drug resistance and disease propagation patterns in the region. This study evaluated the genetic diversity and allele frequencies of msp-1, msp-2 and glurp genes using different molecular analyses (nested PCR, PCR-restriction fragment length polymorphism (RFLP) and sequencing) from 106 autochthonous and imported P. falciparum isolates collected from different endemic areas in Panamá between 2003 and 2019. We also explored if P. falciparum genotypes assessed with these molecular markers were associated with relevant malaria epidemiological parameters using a multiple correspondence analysis. A strong association of certain local haplotypes with their geographic distribution in endemic areas, but also with parasite load and presence of gametocytes, was evidenced. Few multiclonal infections and low genetic diversity among locally transmitted P. falciparum samples were detected, consequent with the low transmission intensity of this parasite in Panamá, a pattern likely to be extended across Mesoamerica. In addition, several imported cases were genetically dissimilar to local infections and representative of more diverse extra-continental lineages.

scholarly journals Low genetic diversity in Wolbachia-Infected Culex quinquefasciatus (Diptera: Culicidae) from Brazil and Argentina

2012 ◽  
Vol 54 (6) ◽  
pp. 325-329 ◽  
Author(s):  
Sirlei Antunes Morais ◽  
Fábio de Almeida ◽  
Lincoln Suesdek ◽  
Mauro Toledo Marrelli
Keyword(s):  
Genetic Diversity ◽  
Culex Quinquefasciatus ◽  
Southern Brazil ◽  
Human Pathogens ◽  
Nuclear Markers ◽  
Low Genetic Diversity ◽  
Geographical Regions ◽  
Filarial Nematodes ◽  
Wolbachia Endosymbiont ◽  
Mtdna Diversity

Culex quinquefasciatus is a vector of human pathogens, including filarial nematodes and several viruses. Although its epidemiological relevance is known to vary across geographical regions, an understanding of its population genetic structure is still incipient. In light of this, we evaluated the genetic diversity of Cx. quinquefasciatus and Cx. pipiens x Cx. quinquefasciatus hybrids collected from nine localities in Brazil and one site in Argentina. We used mitochondrial genes cox1 and nd4, along with the coxA and wsp genes of the maternally-inherited Wolbachia endosymbiont. The nd4 fragment was invariant between samples, whilst cox1 exhibited four haplotypes that separated two types of Cx. quinquefasciatus, one clustered in southern Brazil. Low sequence diversity was generally observed, being discussed. Both Brazilian and Argentinian mosquitoes were infected with a single Wolbachia strain. As reported in previous studies with these populations, cox1 and nd4 diversity is not congruent with the population structure revealed by nuclear markers or alar morphology. Future Cx. quinquefasciatus research should, if possible, evaluate mtDNA diversity in light of other markers.

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