scholarly journals Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America

2021 ◽  
Author(s):  
Bernardo Gutierrez ◽  
Hugo G Castelan ◽  
Darlan da Silva Candido ◽  
Ben Jackson ◽  
Shay Fleishon ◽  
...  
Keyword(s):  
Central America ◽  
Driving Force ◽  
Recombination Event ◽  
Genetic Recombination ◽  
Temporal Distribution ◽  
Genetic Data ◽  
Virus Recombination ◽  
Major Cluster ◽  
The Usa ◽  
Reading Frames

Genetic recombination is an important driving force of coronavirus evolution. While some degree of virus recombination has been reported during the COVID-19 pandemic, previously detected recombinant lineages of SARS-CoV-2 have shown limited circulation and been observed only in restricted areas. Prompted by reports of unusual genetic similarities among several Pango lineages detected mainly in North and Central America, we present a detailed phylogenetic analysis of four SARS-CoV-2 lineages (B.1.627, B.1.628, B.1.631 and B.1.634) in order to investigate the possibility of virus recombination among them. Two of these lineages, B.1.628 and B.1.631, are split into two distinct clusters (here named major and minor). Our phylogenetic and recombination analyses of these lineages find well-supported phylogenetic differences between the Orf1ab region and the rest of the genome (S protein and remaining reading frames). The lineages also contain several deletions in the NSP6, Orf3a and S proteins that can augment reconstruction of reliable evolutionary histories. By reconciling the deletions and phylogenetic data, we conclude that the B.1.628 major cluster originated from a recombination event between a B.1.631 major virus and a lineage B.1.634 virus. This scenario inferred from genetic data is supported by the spatial and temporal distribution of the three lineages, which all co-circulated in the USA and Mexico during 2021, suggesting this region is where the recombination event took place. We therefore support the designation of the B.1.628 major cluster as recombinant lineage XB in the Pango nomenclature. The widespread circulation of lineage XB across multiple countries over a longer timespan than the previously designated recombinant XA lineage raises important questions regarding the role and potential effects of recombination on the evolution of SARS-CoV-2 during the ongoing COVID-19 pandemic.

scholarly journals The Nucleotide Sequence of Shiga Toxin (Stx) 2e-Encoding Phage φP27 Is Not Related to Other Stx Phage Genomes, but the Modular Genetic Structure Is Conserved

2002 ◽  
Vol 70 (4) ◽  
pp. 1896-1908 ◽  
Author(s):  
Jürgen Recktenwald ◽  
Herbert Schmidt
Keyword(s):  
Nucleotide Sequence ◽  
Shiga Toxin ◽  
Phage Genome ◽  
Genetic Recombination ◽  
Genome Structure ◽  
Open Reading Frames ◽  
Functional Modules ◽  
Phage Propagation ◽  
Reading Frames ◽  
Lambdoid Phages

ABSTRACT In this study we determined the complete nucleotide sequence of Shiga toxin 2e-encoding bacteriophage φP27, isolated from the Shiga toxin-producing Escherichia coli patient isolate 2771/97. φP27 is integrated as a prophage in the chromosomal yecE gene. This integration generates identity segments of attL and attR sites with lengths of 11 nucleotides. The integrated prophage genome has a size of 42,575 bp. We identified 58 open reading frames (ORFs), each with a length of >150 nucleotides. The deduced proteins of 44 ORFs showed significant homologies to other proteins present in sequence databases, whereas 14 putative proteins did not. For 29 proteins, we could deduce a putative function. Most of these are related to the basic phage propagation cycle. The φP27 genome represents a mosaic composed of genetic elements which are obviously derived from related and unrelated phages. We identified five short linker sequences of 22 to 151 bp in the φP27 sequence which have also been detected in a couple of other lambdoid phages. These linkers are located between functional modules in the phage genome and are thought to play a role in genetic recombination. Although the overall DNA sequence of φP27 is not highly related to other known phages, the data obtained demonstrate a typical lambdoid genome structure.

scholarly journals Norovirus recombination

2007 ◽  
Vol 88 (12) ◽  
pp. 3347-3359 ◽  
Author(s):  
Rowena A. Bull ◽  
Mark M. Tanaka ◽  
Peter A. White
Keyword(s):  
High Frequency ◽  
Driving Force ◽  
Recombination Event ◽  
Viral Evolution ◽  
Rna Recombination ◽  
Recombination Point ◽  
The Family ◽  
Double Recombination ◽  
Double Recombination Event ◽  
Recombination Breakpoints

RNA recombination is a significant driving force in viral evolution. Increased awareness of recombination within the genus Norovirus of the family Calicivirus has led to a rise in the identification of norovirus (NoV) recombinants and they are now reported at high frequency. Currently, there is no classification system for recombinant NoVs and a widely accepted recombinant genotyping system is still needed. Consequently, there is duplication in reporting of novel recombinants. This has led to difficulties in defining the number and types of recombinants in circulation. In this study, 120 NoV nucleotide sequences were compiled from the current GenBank database and published literature. NoV recombinants and their recombination breakpoints were identified using three methods: phylogenetic analysis, SimPlot analysis and the maximum χ 2 method. A total of 20 NoV recombinant types were identified in circulation worldwide. The recombination point is the ORF1/2 overlap in all isolates except one, which demonstrated a double recombination event within the polymerase region.

scholarly journals Characterizing the Spatial and Temporal Availability of Very High Resolution Satellite Imagery in Google Earth and Microsoft Bing Maps as a Source of Reference Data

Land ◽  
2018 ◽  
Vol 7 (4) ◽  
pp. 118 ◽  
Author(s):  
Myroslava Lesiv ◽  
Linda See ◽  
Juan Laso Bayas ◽  
Tobias Sturn ◽  
Dmitry Schepaschenko ◽  
...  
Keyword(s):  
High Resolution ◽  
Satellite Imagery ◽  
Urban Areas ◽  
Reference Data ◽  
Temporal Distribution ◽  
Google Earth ◽  
Training Data ◽  
Visual Interpretation ◽  
The Usa ◽  
Very High

Very high resolution (VHR) satellite imagery from Google Earth and Microsoft Bing Maps is increasingly being used in a variety of applications from computer sciences to arts and humanities. In the field of remote sensing, one use of this imagery is to create reference data sets through visual interpretation, e.g., to complement existing training data or to aid in the validation of land-cover products. Through new applications such as Collect Earth, this imagery is also being used for monitoring purposes in the form of statistical surveys obtained through visual interpretation. However, little is known about where VHR satellite imagery exists globally or the dates of the imagery. Here we present a global overview of the spatial and temporal distribution of VHR satellite imagery in Google Earth and Microsoft Bing Maps. The results show an uneven availability globally, with biases in certain areas such as the USA, Europe and India, and with clear discontinuities at political borders. We also show that the availability of VHR imagery is currently not adequate for monitoring protected areas and deforestation, but is better suited for monitoring changes in cropland or urban areas using visual interpretation.

Alpha and Rocker - Two Design Approaches that led to the Successful Challenge for the 2007 International C-Class Catamaran Championship

2009 ◽  
Author(s):  
Steve Killing
Keyword(s):  
Cross Section ◽  
Driving Force ◽  
State Of The Art ◽  
Ride Height ◽  
Current State ◽  
New Thinking ◽  
The Usa

In 2007 Canada entered its first challenge for the International C-Class Catamaran Championship and was victorious in capturing the trophy with five straight wins by Alpha CAN 6 over the venerable Cogito from the USA. Two boats were designed for this challenge - the first was Alpha, a wingsail catamaran, which incorporated some new thinking on sail configuration and hull shape. This made it a successful evolutionary, but not revolutionary, step from the current state-of-the-art boats. Compared to Cogito, the main rival, she had a taller, narrower and thinner wing, lighter construction and more circular hull cross section. The second was Rocker, the bold hydrofoil catamaran, using hulls from the same mold as Alpha and an identical wingsail as the driving force. The daggerboard hydrofoils automatically controlled the ride height with trim tabs, while the control of the rudder elevators was left to the helmsman. Although she flew well, was very controllable, and was spectacular to watch, Rocker could not match the 20 knot plus speed of Alpha.

Small Business Collaboration Through Electronic Marketplaces

2011 ◽  
pp. 569-576
Author(s):  
Yin Leng Tan ◽  
Linda Macaulay
Keyword(s):  
Strategic Alliances ◽  
Small Businesses ◽  
Driving Force ◽  
Developed Countries ◽  
Business Sector ◽  
The Usa ◽  
The Uk ◽  
National Economies ◽  
Data Design ◽  
Business Framework

It is widely recognized that small businesses with less than 50 employees make significant contributions to the prosperity of local, regional, and national economies. They are a major source of job creation and a driving force of economic growth for developed countries like the USA (Headd, 2005; SBA, 2005), the UK (Dixon, Thompson, & McAllister, 2002; SBS, 2005), Europe (European Commission, 2003), and developing countries such as China (Bo, 2005). The economic potential is further strengthened when firms collaborate with each other; for example, formation of a supply chain, strategic alliances, or sharing of information and resources (Horvath, 2001; O’Donnell, Cilmore, Cummins, & Carson, 2001; MacGregor, 2004; Todeva & Knoke, 2005). Owing to heterogeneous aspects of small businesses, such as firm size and business sector, a single e-business solution is unlikely to be suitable for all firms (Dixon et al., 2002; Taylor & Murphy, 2004a); however, collaboration requires individual firms to adopt standardized, simplified solutions based on open architectures and data design (Horvath, 2001). The purpose of this article is to propose a conceptual e-business framework and a generic e-catalogue, which enables small businesses to collaborate through the creation of an e-marketplace. To assist with the task, analysis of data from 6,000 small businesses situated within a locality of Greater Manchester, England within the context of an e-business portal is incorporated within this study.

scholarly journals Machine learning challenges and impact: an interview with Thomas Dietterich

2017 ◽  
Vol 5 (1) ◽  
pp. 54-58 ◽  
Author(s):  
Zhi-Hua Zhou
Keyword(s):  
Artificial Intelligence ◽  
Machine Learning ◽  
Driving Force ◽  
Professor Emeritus ◽  
State University ◽  
Learning Society ◽  
Learning Challenges ◽  
The World ◽  
The Usa ◽  
Oregon State University

Abstract Machine learning is the driving force of the hot artificial intelligence (AI) wave. In an interview with NSR, Prof. Thomas Dietterich, the distinguished professor emeritus of computer science at Oregon State University in the USA, the former president of Association of Advancement of Artificial Intelligence (AAAI, the most prestigious association in the field of artificial intelligence) and the founding president of the International Machine Learning Society, talked about exciting recent advances and technical challenges of machine learning, as well as its big impact on the world.

American Asteraceae-feeding Astrotischeria species with a highly modified, three-lobed valva in the male genitalia (Lepidoptera, Tischeriidae)

Zootaxa ◽  
2018 ◽  
Vol 4469 (1) ◽  
pp. 1 ◽  
Author(s):  
JONAS R. STONIS ◽  
ARŪNAS DIŠKUS ◽  
FERNANDO CARVALHO FILHO ◽  
OWEN T. LEWIS
Keyword(s):  
South America ◽  
Central America ◽  
Male Genitalia ◽  
Host Plants ◽  
Trophic Relationships ◽  
Distribution Map ◽  
The North ◽  
The Usa ◽  
First Time ◽  
Asteraceae Family

We review eleven Astrotischeria Puplesis & Diškus (Lepidoptera: Tischeriidae) species which possess a novel character for the Tischeriidae family: a highly modified valva of the male genitalia with one ventral and two dorsal lobes (or processes). The species are distributed in the Americas, including the USA, Caribbean (St. Thomas), Central America (Belize, Guatemala and Honduras), and South America (Ecuador, Bolivia, and Brazil). Species for which the biology has been studied are associated with host plants from Asteroidea of the Asteraceae family. The following seven species are described as new: Astrotischeria trilobata Diškus & Stonis, sp. nov., A. amazonica Diškus & Stonis, sp. nov., A. maya Diškus & Stonis, sp. nov., A. selvica Diškus, Carvalho-Filho & Stonis, sp. nov., A. casila Diškus & Stonis, sp. nov., A. onae Diškus & Stonis, sp. nov., and A. furcata Stonis & Diškus, sp. nov. A new informal species unit, the A. trilobata group, is designated for diagnostic purposes despite some doubts about monophyly of the group. Astrotischeria longeciliata (Frey & Boll) is synonymized here with the North American A. helianthi (Frey & Boll), a species not belonging to the A. trilobata group, syn. nov. For the first time, a method of rearing of adults from mining larvae, specifically adopted for Tischeriidae, is detailed. All species treated in the paper are illustrated with photographs or drawings of the adults, male genitalia, and, if available, the female genitalia, leaf mines and habitats. A distribution map for the species of the A. trilobata group and a scheme of the trophic relationships of the global Tischeriidae fauna are also provided. 

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