scholarly journals Integrated genomic view of SARS-CoV-2 in India

2020 ◽  
Vol 5 ◽  
pp. 184 ◽  
Author(s):  
Pramod Kumar ◽  
Rajesh Pandey ◽  
Pooja Sharma ◽  
Mahesh S. Dhar ◽  
Vivekanand A. ◽  
...  
Keyword(s):  
Host Response ◽  
Genomic Data ◽  
Amplicon Sequencing ◽  
Climatic Conditions ◽  
Molecular Surveillance ◽  
Multiple Introductions ◽  
Oxford Nanopore ◽  
The World ◽  
The Usa ◽  
Local Transmission

Background: India first detected SARS-CoV-2, causal agent of COVID-19 in late January 2020, imported from Wuhan, China. From March 2020 onwards, the importation of cases from countries in the rest of the world followed by seeding of local transmission triggered further outbreaks in India. Methods: We used ARTIC protocol-based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT sequencing from Oxford Nanopore Technology to understand how introduction and local transmission occurred. Results: The analyses revealed multiple introductions of SARS-CoV-2 genomes, including the A2a cluster from Europe and the USA, A3 cluster from Middle East and A4 cluster (haplotype redefined) from Southeast Asia (Indonesia, Thailand and Malaysia) and Central Asia (Kyrgyzstan). The local transmission and persistence of genomes A4, A2a and A3 was also observed in the studied locations. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, and are here proposed as A4-clade based on its divergence within the A cluster. Conclusions: The viral haplotypes may link their persistence to geo-climatic conditions and host response. Multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.

scholarly journals Integrated genomic view of SARS-CoV-2 in India

2020 ◽  
Author(s):  
Pramod Kumar ◽  
Rajesh Pandey ◽  
Pooja Sharma ◽  
Mahesh S Dhar ◽  
A Vivekanand ◽  
...  
Keyword(s):  
Real Time ◽  
Host Response ◽  
Genomic Data ◽  
Amplicon Sequencing ◽  
Climatic Conditions ◽  
Therapeutic Interventions ◽  
Molecular Surveillance ◽  
Multiple Introductions ◽  
Oxford Nanopore ◽  
Local Transmission

SUMMARYIndia first detected SARS-CoV-2, causal agent of COVID-19 in late January-2020, imported from Wuhan, China. March-2020 onwards; importation of cases from rest of the countries followed by seeding of local transmission triggered further outbreaks in India. We used ARTIC protocol based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT from Oxford Nanopore Technology to understand introduction and local transmission. The analyses revealed multiple introductions of SARS-CoV-2 from Europe and Asia following local transmission. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, here, proposed as A4-clade based on its divergence within A-cluster. The viral haplotypes may link their persistence to geo-climatic conditions and host response. Despite the effectiveness of non-therapeutic interventions in India, multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.

scholarly journals Detection of SARS-CoV-2 variant 501Y.V2 in Comoros Islands in January 2021

2021 ◽  
Vol 6 ◽  
pp. 192
Author(s):  
Charles N. Agoti ◽  
George Githinji ◽  
Khadija S. Mohammed ◽  
Arnold W. Lambisia ◽  
Zaydah R. de Laurent ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Control Strategies ◽  
Close Association ◽  
Genomic Data ◽  
Recent Common Ancestor ◽  
Major Infection ◽  
Multiple Introductions ◽  
Most Recent Common Ancestor ◽  
The Indian Ocean ◽  
Local Transmission

Background. Genomic data is key in understanding the spread and evolution of SARS-CoV-2 pandemic and informing the design and evaluation of interventions. However, SARS-CoV-2 genomic data remains scarce across Africa, with no reports yet from the Indian Ocean islands. Methods. We genome sequenced six SARS-CoV-2 positive samples from the first major infection wave in the Union of Comoros in January 2021 and undertook detailed phylogenetic analysis. Results. All the recovered six genomes classified within the 501Y.V2 variant of concern (also known as lineage B.1.351) and appeared to be from 2 sub-clusters with the most recent common ancestor dated 30th Oct-2020 (95% Credibility Interval: 06th Sep-2020 to 10th Dec-2020). Comparison of the Comoros genomes with those of 501Y.V2 variant of concern from other countries deposited into the GISAID database revealed their close association with viruses identified in France and Mayotte (part of the Comoros archipelago and a France, Overseas Department). Conclusions. The recovered genomes, albeit few, confirmed local transmission following probably multiple introductions of the SARS-CoV-2 501Y.V2 variant of concern during the Comoros’s first major COVID-19 wave. These findings demonstrate the importance of genomic surveillance and have implications for ongoing control strategies on the islands.

scholarly journals Molecular surveillance of zoonotic bacterial pathogens in farm dwelling peridomestic rodents across the upper Midwest, USA

2021 ◽  
Author(s):  
Nusrat A. Jahan ◽  
Laramie L. Lindsey ◽  
Evan J. Kipp ◽  
Bradley J Heins ◽  
Amy M. Runck ◽  
...  
Keyword(s):  
Foodborne Pathogens ◽  
Amplicon Sequencing ◽  
Effective Control ◽  
Human Pathogens ◽  
Blarina Brevicauda ◽  
Food Borne ◽  
16S Amplicon Sequencing ◽  
Oxford Nanopore ◽  
Animal Farms ◽  
The Usa

The effective control of rodent populations on farms is a critical component of food-safety, as rodents are reservoirs and vectors for many foodborne pathogens in addition to several zoonotic pathogens. The functional role of rodents in the amplification and transmission of pathogens is likely underappreciated. Clear links have been identified between rodents and outbreaks of pathogens throughout Europe and Asia, however, comparatively little research has been devoted to studying this rodent-agricultural interface in the USA, particularly across the Midwest. Here, we address this existing knowledge gap by characterizing the metagenomic communities of rodent pests collected from Minnesota and Wisconsin food animal farms. We leveraged the Oxford Nanopore MinION sequencer to provide a rapid real-time survey of the putative zoonotic food-borne and other human pathogens. Rodents (mice and rats) were live trapped from three dairy and mixed animal farms. Tissues and fecal samples were collected from all rodents. DNA extraction was performed on 90 rodent colons along with 2 shrew colons included as outgroups in the study. Full-length 16S amplicon sequencing was performed with the MinION. Our data suggests the presence of putative foodborne pathogens including Salmonella spp., Campylobacter spp., Staphylococcus aureus, and Clostridium spp., along with many important mastitis pathogens. A critically important observation is that we discovered these pathogens within all five species of rodents (Microtus pennsylvanicus, Mus musculus, Peromyscus leucopus, Peromyscus maniculatus, and Rattus norvegicus) and shrew (Blarina brevicauda) in varying abundances. Interestingly, we observed a higher abundance of enteric pathogens (e.g. Salmonella) in shrew feces compared to the rodents analyzed in our study, however more data is required to establish that connection. Knowledge gained from our research efforts will directly inform and improve upon farm-level biosecurity efforts and public health interventions to reduce future outbreaks of foodborne and zoonotic disease.

scholarly journals Multiple introductions followed by ongoing community spread of SARS-CoV-2 at one of the largest metropolitan areas in the Northeast of Brazil

2020 ◽  
Author(s):  
Marcelo Henrique Santos Paiva ◽  
Duschinka Ribeiro Duarte Guedes ◽  
Cassia Docena ◽  
Matheus Filgueira Bezerra ◽  
Filipe Zimmer Dezordi ◽  
...  
Keyword(s):  
Metropolitan Areas ◽  
The State ◽  
Genomic Sequences ◽  
Virus Infectivity ◽  
Protein Amino Acid ◽  
Multiple Introductions ◽  
Phylogenetic Reconstructions ◽  
The World ◽  
The Usa ◽  
Affected Country

The emergence of SARS-CoV-2 in the human population has caused a huge pandemic that is still unfolding in many countries around the world. Multiple epicenters of the pandemic have emerged since the first pneumonia cases in Wuhan, first in Italy followed by the USA and Brazil. Up to now, Brazil is the second most affected country, however, genomic sequences of SARS-CoV-2 strains circulating in the country are restricted to some highly impacted states. Although the Pernambuco state, located in the Northeast Region, is the sixth most affected brazilian state and the second considering lethality rate, there is a lack of high quality genomic sequences from the strains circulating in this region. Here, we sequenced 38 strains of SARS-CoV-2 from patients presenting Covid-19 symptoms. Phylogenetic reconstructions revealed that three lineages were circulating in the state and 36 samples belong to B1.1 lineage. We detected two introductions from European countries and five clades, corroborating the community spread of the virus between different municipalities of the state. Finally, we detected that all except one strain showed the D614G spike protein amino acid change that may impact virus infectivity in human cells. Our study brought new light to the spread of SARS-CoV-2 strains in one of the most heavily impacted states of Brazil.

scholarly journals Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic Rodents

Pathogens ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1183
Author(s):  
Nusrat A. Jahan ◽  
Laramie L. Lindsey ◽  
Evan J. Kipp ◽  
Adam Reinschmidt ◽  
Bradley J. Heins ◽  
...  
Keyword(s):  
Foodborne Pathogens ◽  
Amplicon Sequencing ◽  
Effective Control ◽  
Salmonella Spp ◽  
Blarina Brevicauda ◽  
Farm Level ◽  
16S Amplicon Sequencing ◽  
Oxford Nanopore ◽  
Animal Farms ◽  
The Usa

The effective control of rodent populations on farms is crucial for food safety, as rodents are reservoirs and vectors for several zoonotic pathogens. Clear links have been identified between rodents and farm-level outbreaks of pathogens throughout Europe and Asia; however, comparatively little research has been devoted to studying the rodent–agricultural interface in the USA. Here, we address this knowledge gap by metabarcoding bacterial communities of rodent pests collected from Minnesota and Wisconsin food animal farms. We leveraged the Oxford Nanopore MinION sequencer to provide a rapid real-time survey of putative zoonotic foodborne pathogens, among others. Rodents were live trapped (n = 90) from three dairy and mixed animal farms. DNA extraction was performed on 63 rodent colons along with 2 shrew colons included as outgroups in the study. Full-length 16S amplicon sequencing was performed. Our farm-level rodent-metabarcoding data indicate the presence of multiple foodborne pathogens, including Salmonella spp., Campylobacter spp., Staphylococcus aureus, and Clostridium spp., along with many mastitis pathogens circulating within five rodent species (Microtus pennsylvanicus, Mus musculus, Peromyscus leucopus, Peromyscus maniculatus, and Rattus norvegicus) and a shrew (Blarina brevicauda). Interestingly, we observed a higher abundance of enteric pathogens (e.g., Salmonella) in shrew feces compared to the rodents analyzed in our study. Knowledge gained from our research efforts will directly inform and improve farm-level biosecurity efforts and public health interventions to reduce future outbreaks of foodborne and zoonotic disease.

Optimum Structure of the Banking Market: How Many Banks Are Necessary for Russia?

2006 ◽  
pp. 75-92 ◽  
Author(s):  
S. Moiseev
Keyword(s):  
Banking Sector ◽  
Optimum Structure ◽  
Population Number ◽  
The Third ◽  
Banking Market ◽  
The World ◽  
The Usa ◽  
Per Capita ◽  
The Empirical Analysis ◽  
Equilibrium Number

The number of classical banks in the world has reduced. In the majority of countries the number of banks does not exceed 200. The uniqueness of the Russian banking sector is that in this respect it takes the third place in the world after the USA and Germany. The paper reviews the conclusions of the economic theory about the optimum structure of the banking market. The empirical analysis shows that the number of banks in a country is influenced by the size of its territory, population number and GDP per capita. Our econometric estimate is that the equilibrium number of banks in Russia should be in a range of 180-220 units.

Russian Banking Sector under World Financial Market Uncertainty: Problems and Prospects

2008 ◽  
pp. 4-19 ◽  
Author(s):  
A. Ulyukaev ◽  
E. Danilova
Keyword(s):  
Emerging Markets ◽  
Financial Market ◽  
Banking Sector ◽  
Financial System ◽  
Local Market ◽  
Market Uncertainty ◽  
Balanced Growth ◽  
Banking Sector Development ◽  
The World ◽  
The Usa

The authors point out that the local market crisis - on the USA substandard loan market - has led to the uncertainty of the world financial market. It has caused the growing demand for liquidity in the framework of the world financial system. The Russian banking sector seems to be more stable under negative changes than banking systems of other emerging markets. At the same time one can assume that the crisis will become the factor of qualitative shift in the character of the Russian banking sector development - the shift from impetuous to more balanced growth.

9/11 and Armageddon: the Christian Right and George W. Bush

2003 ◽  
Vol 2 (1) ◽  
pp. 33-50
Author(s):  
Göran Gunner
Keyword(s):  
New York ◽  
Christian Right ◽  
Political Life ◽  
Religious Leader ◽  
The European Union ◽  
The World ◽  
Mega Church ◽  
The Usa ◽  
Jerry Falwell ◽  
High Degree

Authors from the Christian Right in the USA situate the September 11 attack on New York and Washington within God's intentions to bring America into the divine schedule for the end of the world. This is true of Pat Robertson and Jerry Falwell, and other leading figures in the ‘Christian Coalition’. This article analyses how Christian fundamentalists assess the roles of the USA, the State of Israel, Islam, Iraq, the European Union and Russia within what they perceive to be the divine plan for the future of the world, especially against the background of ‘9/11’. It argues that the ideas of the Christian Right and of President George W. Bush coalesce to a high degree. Whereas before 9/11 many American mega-church preachers had aspirations to direct political life, after the events of that day the President assumes some of the roles of a mega-religious leader.

Sandra Ramos Revisited

2020 ◽  
Vol 2 (4) ◽  
pp. 32-54
Author(s):  
Silvia Spitta
Keyword(s):  
United States ◽  
The United States ◽  
Ancient Greek ◽  
Graphic Arts ◽  
Left Behind ◽  
The World ◽  
The Usa ◽  
Political Choices ◽  
The Rich

Sandra Ramos (b. 1969) is one of the few artists to reflect critically on both sides of the Cuban di-lemma, fully embodying the etymological origins of the word in ancient Greek: di-, meaning twice, and lemma, denoting a form of argument involving a choice between equally unfavorable alternatives. Throughout her works she shines a light on the dilemmas faced by Cubans whether in Cuba or the United States, underlining the bad personal and political choices people face in both countries. During the hard 1990s, while still in Havana, the artist focused on the traumatic one-way journey into exile by thousands, as well as the experience of profound abandonment experienced by those who were left behind on the island. Today she lives in Miami and operates a studio there as well as one in Havana. Her initial disorientation in the USA has morphed into an acerbic representation and critique of the current administration and a deep concern with the environmental collapse we face. A buffoonlike Trumpito has joined el Bobo de Abela and Liborio in her gallery of comic characters derived from the rich Cuban graphic arts tradition where she was formed. While Cuba is now represented as a rotten cake with menacing flies hovering over it ready to pounce, a bombastic Trumpito marches across the world stage, trampling everything underfoot, a dollar sign for a face.

Sign in / Sign up

Export Citation Format

Share Document