scholarly journals CovidPhy: A tool for phylogeographic analysis of SARS-CoV-2 variation

2021 ◽  
pp. 111909
Author(s):  
Xabier Bello ◽  
Jacobo Pardo-Seco ◽  
Alberto Gómez-Carballa ◽  
Hansi Weissensteiner ◽  
Federico Martinón-Torres ◽  
...  
Keyword(s):  
Phylogeographic Analysis

scholarly journals Genomic Analysis of Avian Infectious Bronchitis Viruses Recently Isolated in South Korea Reveals Multiple Introductions of GI-19 Lineage (QX Genotype)

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1045
Author(s):  
Hyuk-Chae Lee ◽  
Sol Jeong ◽  
Andrew Y. Cho ◽  
Kyu-Jik Kim ◽  
Jun-Young Kim ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
South Korea ◽  
Infectious Bronchitis Virus ◽  
Economic Burden ◽  
Genomic Analysis ◽  
Multiple Introductions ◽  
Infectious Bronchitis ◽  
South Korean ◽  
Phylogeographic Analysis ◽  
The Past

Infectious bronchitis virus (IBV) was first identified in the 1930s and it imposes a major economic burden on the poultry industry. In particular, GI-19 lineage has spread globally and has evolved constantly since it was first detected in China. In this study, we analyzed S1 gene sequences from 60 IBVs isolated in South Korea. Two IBV lineages, GI-15 and GI-19, were identified in South Korea. Phylogenetic analysis suggested that there were six distinct subgroups (KM91-like, K40/09-like, and QX-like I to IV) of the South Korean GI-19 IBVs. Among them, QX-type III and IV subgroups, which are phylogenetically different from those reported in South Korea in the past, accounted for more than half of the total. Moreover, the phylogeographic analysis of the QX-like subgroups indicated at least four distinct introductions of GI-19 IBVs into South Korea during 2001–2020. The efficacy of commercialized vaccines against the recently introduced QX-like subgroups should be verified, and continuous international surveillance efforts and quarantine procedures should be enhanced to prevent the incursion of viruses.

Phylogeographic analysis of the Bufo gargarizans species complex: A revisit

2005 ◽  
Vol 37 (1) ◽  
pp. 202-213 ◽  
Author(s):  
Jinzhong Fu ◽  
Cameron J. Weadick ◽  
Xiaomao Zeng ◽  
Yuezhao Wang ◽  
Zhijun Liu ◽  
...  
Keyword(s):  
Species Complex ◽  
Phylogeographic Analysis ◽  
Bufo Gargarizans

On the falsifiability of the nested clade phylogeographic analysis method

2008 ◽  
Vol 17 (6) ◽  
pp. 1404-1404 ◽  
Author(s):  
RÉMY J. PETIT
Keyword(s):  
Analysis Method ◽  
Phylogeographic Analysis

Phylogeographic analysis of Japanese encephalitis virus in India (1956-2012)

2015 ◽  
Vol 160 (12) ◽  
pp. 3097-3104 ◽  
Author(s):  
Sarah S. Cherian ◽  
A. M. Walimbe
Keyword(s):  
Japanese Encephalitis Virus ◽  
Japanese Encephalitis ◽  
Encephalitis Virus ◽  
Phylogeographic Analysis

scholarly journals Phylogeographic Analysis Reveals Multiple International transmission Events Have Driven the Global Emergence of Escherichia coli O157:H7

2018 ◽  
Vol 69 (3) ◽  
pp. 428-437 ◽  
Author(s):  
Eelco Franz ◽  
Ovidiu Rotariu ◽  
Bruno S Lopes ◽  
Marion MacRae ◽  
James L Bono ◽  
...  
Keyword(s):  
United States ◽  
Disease Outbreaks ◽  
The United States ◽  
Human Case ◽  
Whole Genome Sequencing Data ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
E Coli ◽  
Phylogeographic Analysis ◽  
International Distribution

AbstractBackgroundShiga toxin–producing Escherchia coli (STEC) O157:H7 is a zoonotic pathogen that causes numerous food and waterborne disease outbreaks. It is globally distributed, but its origin and the temporal sequence of its geographical spread are unknown.MethodsWe analyzed whole-genome sequencing data of 757 isolates from 4 continents, and performed a pan-genome analysis to identify the core genome and, from this, extracted single-nucleotide polymorphisms. A timed phylogeographic analysis was performed on a subset of the isolates to investigate its worldwide spread.ResultsThe common ancestor of this set of isolates occurred around 1890 (1845–1925) and originated from the Netherlands. Phylogeographic analysis identified 34 major transmission events. The earliest were predominantly intercontinental, moving from Europe to Australia around 1937 (1909–1958), to the United States in 1941 (1921–1962), to Canada in 1960 (1943–1979), and from Australia to New Zealand in 1966 (1943–1982). This pre-dates the first reported human case of E. coli O157:H7, which was in 1975 from the United States.ConclusionsInter- and intra-continental transmission events have resulted in the current international distribution of E. coli O157:H7, and it is likely that these events were facilitated by animal movements (eg, Holstein Friesian cattle). These findings will inform policy on action that is crucial to reduce the further spread of E. coli O157:H7 and other (emerging) STEC strains globally.

scholarly journals Molecular analysis of populations of the invasive species Rhynchophorus ferrugineus Olivier, 1790 (Coleoptera: Curculionidae) in the Region of Murcia (Spain)

2017 ◽  
pp. 155-176
Author(s):  
Miguel Lozano-Terol ◽  
María Juliana Rodríguez-García ◽  
José Galián
Keyword(s):  
Invasive Species ◽  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Molecular Analysis ◽  
Cox1 Gene ◽  
Rhynchophorus Ferrugineus ◽  
Phylogeographic Analysis ◽  
Oxidase Subunit

En este estudio se analizan dos fragmentos del gen de la citocromo c oxidasa subunidad I (COX1) del ADN mitocondrial de 61 individuos del género Rhynchophorus colectados en la Región de Murcia a fin de determinar su procedencia. El análisis filogenético del fragmento 1 de las muestras de la Región de Murcia conjuntamente con las secuencias disponibles en GenBank indica que los individuos corresponden a la especie Rhynchophorus ferrugineus.Las secuencias de Murcia se colapsan en un único haplotipo (H8 mediterráneo) que aparece dentro del clado de R. ferrugineus. De los análisis filogeográficos se infiere que el origen de los individuos de Murcia es Egipto. Adicionalmente, se examinó una región contigua del COX1 (fragmento 2) en la que las secuencias se colapsaron en dos haplotipos. In this research two fragments of the cytochrome c oxidase subunit I (COX1) gene of the mitochondrial DNA were analyzed in 61 individuals of the genus Rhynchophorus collected in the Region of Murcia with the aim of determining their origin. Phylogenetic analysis of fragment 1 of the samples collected in the Region of Murcia together with the available sequences in GenBank, indicated that these individuals correspond to the species R. ferrugineus. Sequences from Murcia collapsed into the H8 Mediterranean haplotype, which cluster into the R. ferrugineus clade. Phylogeographic analysis shows that the origin of the individuals collected in the Region of Murcia is Egypt. Additionally, a contiguous fragment of COX1 (fragment 2) was analyzed and the sequences collapsed into two haplotypes.

Phylogeographic analysis on the travel-related introduction of HIV-1 non-B subtypes to Northern Poland

2014 ◽  
Vol 27 ◽  
pp. 121-130 ◽  
Author(s):  
Milosz Parczewski ◽  
Anna Urbanska ◽  
Anna Grzeszczuk ◽  
Katarzyna Maciejewska ◽  
Magdalena Witak-Jedra ◽  
...  
Keyword(s):  
Phylogeographic Analysis ◽  
Northern Poland ◽  
Hiv 1

scholarly journals Phylogeographic Analysis of Blastomyces dermatitidis and Blastomyces gilchristii Reveals an Association with North American Freshwater Drainage Basins

PLoS ONE ◽  
2016 ◽  
Vol 11 (7) ◽  
pp. e0159396 ◽  
Author(s):  
Lisa R. McTaggart ◽  
Elizabeth M. Brown ◽  
Susan E. Richardson
Keyword(s):  
North American ◽  
Blastomyces Dermatitidis ◽  
Drainage Basins ◽  
Phylogeographic Analysis ◽  
North American Freshwater

Phylogeographic analysis of Thyrsites atun (Perciformes: Gempylidae) reveals connectivity between fish from South Africa and Chile

2021 ◽  
Vol 17 (4) ◽  
pp. 401-413
Author(s):  
Mathias Hüne ◽  
Pablo A. Oyarzún ◽  
Pablo Reyes ◽  
Gladys Rivera ◽  
Mario Montecinos
Keyword(s):  
South Africa ◽  
Phylogeographic Analysis
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