scholarly journals Whole-Genome Sequences of SARS-CoV-2 Isolates from Ethiopian Patients

2021 ◽  
Vol 10 (38) ◽  
Author(s):  
Dawit Hailu Alemayehu ◽  
Bethlehem Adnew ◽  
Fekadu Alemu ◽  
Dessalegn Abeje Tefera ◽  
Tamrayehu Seyoum ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Genetic Group ◽  
The Other ◽  
Whole Genome ◽  
Genome Sequences

Three complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Ethiopian patients were compared with deposited global genomes. Two genomes belonged to genetic group 20A/B.1/GH, and the other belonged to genetic group 20A/B.1.480/GH. Enhancing genomic capacity is important to investigate the transmission and to monitor the evolution and mutational patterns of SARS-CoV-2 in this country.

scholarly journals Surge of severe acute respiratory syndrome coronavirus 2 infections linked to single introduction of a virus strain in Myanmar, 2020

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Myat Htut Nyunt ◽  
Hnin Ohnmar Soe ◽  
Kay Thi Aye ◽  
Wah Wah Aung ◽  
Yi Yi Kyaw ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Early Phase ◽  
International Travel ◽  
Health Concern ◽  
Whole Genome ◽  
Genome Sequences ◽  
Genomic Epidemiology ◽  
Local Spread ◽  
Control And Prevention ◽  
Local Transmission

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a major health concern globally. Genomic epidemiology is an important tool to assess the pandemic of coronavirus disease 2019 (COVID-19). Several mutations have been reported by genome analysis of the SARS-CoV-2. In the present study, we investigated the mutational and phylogenetic analysis of 30 whole-genome sequences for the virus's genomic characteristics in the specimens collected in the early phase of the pandemic (March–June, 2020) and the sudden surge of local transmission (August–September, 2020). The four samples in the early phase of infection were B.6 lineage and located within a clade of the samples collected at the same time in Singapore and Malaysia, while five returnees by rescue flights showed the lineage B. 1.36.1 (three from India), B.1.1 (one from India) and B.1.80 (one from China). However, there was no evidence of local spread from these returnees. Further, all 19 whole-genome sequences collected in the sudden surge of local transmission showed lineage B.1.36. The surge of the second wave on SARS-CoV-2 infection was linked to the single-introduction of a variant (B.1.36) that may result from the strict restriction of international travel and containment efforts. These genomic data provides the useful information to disease control and prevention strategy.

scholarly journals Complete Genome Sequences of Three Streptococcus agalactiae Serotype Ia Isolates Obtained from Disease Outbreaks in Nile Tilapia (Oreochromis niloticus)

2018 ◽  
Vol 6 (1) ◽  
Author(s):  
Anita Jaglarz ◽  
Artur Gurgul ◽  
William J. Leigh ◽  
Janina Z. Costa ◽  
Kim D. Thompson
Keyword(s):  
United States ◽  
Streptococcus Agalactiae ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Disease Outbreaks ◽  
The United States ◽  
The Other ◽  
Whole Genome ◽  
Genome Sequences ◽  
Nile Tilapia Oreochromis Niloticus

ABSTRACT This paper describes the whole-genome sequences for three Streptococcus agalactiae serotype Ia isolates. The isolates were recovered from the brains of clinically sick tilapia, Oreochromis niloticus, that were suffering from streptococcosis. One isolate was from tilapia in the United States and the other two from fish in China.

scholarly journals Evolution of an Eleusine-Specific Subgroup of Pyricularia oryzae Through a Gain of an Avirulence Gene

2020 ◽  
Vol 33 (2) ◽  
pp. 153-165
Author(s):  
Soichiro Asuke ◽  
Masaki Tanaka ◽  
Gang-Su Hyon ◽  
Yoshihiro Inoue ◽  
Trinh Thi Phuong Vy ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Finger Millet ◽  
Phylogenetic Analyses ◽  
Pyricularia Oryzae ◽  
The Other ◽  
Avirulence Gene ◽  
Whole Genome ◽  
Genome Sequences ◽  
Specific Subgroup ◽  
Dna Fragment

Eleusine isolates (members of the Eleusine pathotype) of Pyricularia oryzae are divided into two subgroups, EC-I and EC-II, differentiated by molecular markers. A multilocus phylogenetic analysis revealed that these subgroups are very close to Eragrostis isolates. EC-II and Eragrostis isolates were exclusively virulent on finger millet and weeping lovegrass, respectively, while EC-I isolates were virulent on both. The avirulence of EC-II on weeping lovegrass was conditioned by an avirulence gene, PWL1. All EC-II isolates shared a peculiar structure (P structure) that was considered to be produced by an insertion (or translocation) of a DNA fragment carrying PWL1. On the other hand, all EC-I and Eragrostis isolates were noncarriers of PWL1 and shared a gene structure that should have predated the insertion of the PWL1-containing fragment. These results, together with phylogenetic analyses using whole-genome sequences, suggest that the Eleusine-specific subgroup (EC-II) evolved through a loss of pathogenicity on weeping lovegrass caused by a gain of PWL1.

scholarly journals Evolutionary and genomic analysis of four SARS-CoV-2 isolates circulating in March 2020 in Sri Lanka; Additional evidence on multiple introduction and further transmission

2021 ◽  
Vol 149 ◽  
Author(s):  
Dilan Amila Satharasinghe ◽  
Parakatawella Mudiyanselage Shalini Daupadi Kumari Parakatawella ◽  
Jayasekara Mudiyanselage Krishanthi Jayarukshi Kumari Premarathne ◽  
L. J. P. Anura P. Jayasooriya ◽  
Gamika A. Prathapasinghe ◽  
...  
Keyword(s):  
Sri Lanka ◽  
Disease Transmission ◽  
Genomic Analysis ◽  
Virus Evolution ◽  
Control Measures ◽  
The Other ◽  
Whole Genome ◽  
Genome Sequences ◽  
Main Cluster ◽  
Multiple Introduction

Abstract The molecular epidemiology of the virus and mapping helps understand the epidemics' evolution and apply quick control measures. This study provides genomic evidence of multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) introductions into Sri Lanka and virus evolution during circulation. Whole-genome sequences of four SARS-CoV-2 strains obtained from coronavirus disease 2019 (COVID-19) positive patients reported in Sri Lanka during March 2020 were compared with sequences from Europe, Asia, Africa, Australia and North America. The phylogenetic analysis revealed that the sequence of the sample of the first local patient collected on 10 March, who contacted tourists from Italy, was clustered with SARS-CoV-2 strains collected from Italy, Germany, France and Mexico. Subsequently, the sequence of the isolate obtained on 19 March also clustered in the same group with the samples collected in March and April from Belgium, France, India and South Africa. The other two strains of SARS-CoV-2 were segregated from the main cluster, and the sample collected from 16 March clustered with England and the sample collected on 30 March showed the highest genetic divergence to the isolate of Wuhan, China. Here we report the first molecular epidemiological study conducted on circulating SARS-CoV-2 in Sri Lanka. The finding provides the robustness of molecular epidemiological tools and their application in tracing possible exposure in disease transmission during the pandemic.

scholarly journals Whole-Genome Sequences of SARS-CoV-2 Isolates from the Dominican Republic

2021 ◽  
Vol 10 (47) ◽  
Author(s):  
R. Paulino-Ramirez ◽  
E. Riego ◽  
A. Vallejo-Degaudenzi ◽  
V. V. Calderon ◽  
L. Tapia ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Flow ◽  
Severe Acute Respiratory Syndrome ◽  
Dominican Republic ◽  
Molecular Diversity ◽  
Whole Genome ◽  
Genome Sequences ◽  
Starting Point ◽  
Genomic Studies ◽  
The Caribbean

Here, we report the genome sequences of five severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains that were obtained from symptomatic individuals with travel histories during community surveillance in the Dominican Republic in 2020. These sequences provide a starting point for further genomic studies of gene flow and molecular diversity in the Caribbean nation. Phylogenetic analysis suggests that all genomes correspond to the B.1 variant.

scholarly journals Surge of Severe Acute Respiratory Syndrome Coronavirus 2 Infections Linked to Single Introduction of a Virus Strain in Myanmar, 2020

2020 ◽  
Author(s):  
Myat Htut Nyunt ◽  
Hnin Ohnmar Soe ◽  
Kay Thi Aye ◽  
Wah Wah Aung ◽  
Yi Yi Kyaw ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Severe Acute Respiratory Syndrome ◽  
Early Stage ◽  
International Travel ◽  
Health Concern ◽  
Whole Genome ◽  
Genome Sequences ◽  
Genomic Epidemiology ◽  
Control And Prevention ◽  
Local Transmission

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a major health concern globally. Genomic epidemiology is an important tool to assess the pandemic of the coronavirus disease 2019 (COVID-19). Several mutations have been reported by genome analysis of the SARS-CoV-2. In the present study, we investigate mutational and phylogenetic analysis of 30 whole genome sequences for genomic characteristics of the virus in the specimens collected early phase of pandemic, (March-June, 2020) and sudden surge of infection (August-September, 2020). Phylogenetic analysis revealed that 4 samples of L strain and 1 GR strain in early stage of local transmission, while 6 returnees by rescue flights showed GH (India) and GR strains (China and Philippines) with no evidence of local spread. However, all 19 whole genome sequences in sudden surge of local transmission showed genetically distinct clade GH (Lineage B.1.36). Surge of second wave on SARS-CoV-2 infection was linked to the single-introduction of the GH strain that may be a result of strict restriction of international travel and containment efforts. These genomic data provides the useful information to disease control and prevention strategy.

scholarly journals Draft Genome Sequences of Four Plant Probiotic Bacillus Strains: TABLE 1 

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Haeyoung Jeong ◽  
Seung-Hwan Park ◽  
Soo-Keun Choi
Keyword(s):  
Draft Genome ◽  
The Other ◽  
Whole Genome ◽  
Genome Sequences ◽  
Bacillus Endophyticus ◽  
Type Strains ◽  
Bacillus Strains

Here, we report the whole-genome sequences of four Bacillus strains that exhibit plant probiotic activities. Three of them are the type strains of Bacillus endophyticus , “ Bacillus gaemokensis ,” and Bacillus trypoxylicola , and the other, Bacillus sp. strain KCTC 13219, should be reclassified into a species belonging to the genus Lysinibacillus .

scholarly journals Evolutionary and genomic analysis of four SARS-CoV-2 isolates circulating in March 2020 in Sri Lanka; Additional evidence on multiple introduction and further transmission

2020 ◽  
Author(s):  
Dilan Amila Satharasinghe ◽  
Parakatawella Mudiyanselage Shalini Daupadi Kumari Parakatawella ◽  
Jayasekara Mudiyanselage Krishanthi Jayarukshi Kumari Premarathne ◽  
L. J.P. Anura P. Jayasooriya ◽  
Gamika A. Prathapasinghe ◽  
...  
Keyword(s):  
Sri Lanka ◽  
Disease Transmission ◽  
Genomic Analysis ◽  
Virus Evolution ◽  
Control Measures ◽  
The Other ◽  
Whole Genome ◽  
Genome Sequences ◽  
Main Cluster ◽  
Multiple Introduction

Abstract The molecular epidemiology of the virus, and mapping help to understand the evolution of the epidemics and apply quick control measures. The study genomic evidence of multiple SARS-CoV-2 introductions into Sri Lanka and virus evolution during circulation. Whole-genome sequences of four SARS-CoV-2 strains obtained from COVID-19 positive patients reported in Sri Lanka during March 2020 were compared with sequences from Europe and elsewhere. The phylogenetic analysis revealed that the sequence of the sample of first local patient collected on 10th March, who contacted tourists from Italy, was clustered with SARS-CoV-2 strains collected from Italy, Germany, France and Mexico. Subsequently, the sequence of the isolate obtained on 19th March also clustered in the same group with the samples collected in March and April from Belgium, France, India, and South Africa. The other two strains of SARS-CoV-2 were segregated from the main cluster, and the sample collected from 16th March clustered with England and the sample collected on 30th March showed the highest genetic divergent to the isolate of Wuhan, China. Here we report the first molecular epidemiological study conducted on circulating SARS-CoV-2 in Sri Lanka. The finding provides the robustness of molecular epidemiological tools and its application in tracing possible exposure in disease transmission during the pandemic.

scholarly journals Geographic and Phylodynamic Distribution of SARS-CoV-2 from Environmental Origin

2021 ◽  
Author(s):  
Elijah Kolawole Oladipo ◽  
Boluwatife Ayobami Irewolede ◽  
Precious Moyosoluwa Oyewole ◽  
Emmanuel Oluwatobi Dairo ◽  
Ayodele Eugene Ayeni ◽  
...  
Keyword(s):  
United States ◽  
Severe Acute Respiratory Syndrome ◽  
Common Ancestor ◽  
Evolutionary Process ◽  
Geographic Location ◽  
The United States ◽  
Transmission Dynamics ◽  
Whole Genome ◽  
Genome Sequences ◽  
Phylodynamic Analysis

The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally. Understanding the transmission dynamics of SARS-CoV-2 contamination in the environment is essential for infection control policies. This study aims to provide a phylodynamic analysis and distribution pattern of SARS-CoV-2 from the environment in terms of Source, clades, lineages, and their location. Ninety (90) retrieved whole-genome sequences of environmental sources from GISAID were investigated to determine the evolutionary process of SARS-CoV-2 and mutation in the isolated nucleotide sequences. The analysis was carried out using R, MAFFT, and MEGA X software. Out of the five countries studied, Austria has the highest distribution with sixty-five samples (72.2%), and the highest isolates of 68 (75.6%) were from raw sewage. The highest clade in circulation as obtained from the study is G with lineages B. The phylogeny of SARS-CoV-2 whole-genome sequences from Austria, the United States, China, Brazil, and Liechtenstein indicated that the SARS-CoV-2 viruses were all clustered together, irrespective of sequence geographic location. The study concluded by demonstrating a clear interconnection between the phylogeny of SARS-CoV-2 isolates from various geographic locations, all of which were locked in the same cluster regardless of their environment specimen. Thus, depicting the possibility of their origination from a common ancestor.

scholarly journals Whole-Genome Sequences of SARS-CoV-2 Lineage B.1.525 Strains (Variant η) Detected from Patients in the Abruzzo Region (Central Italy) during Spring 2021

2021 ◽  
Vol 10 (31) ◽  
Author(s):  
Emiliano Delli Compagni ◽  
Iolanda Mangone ◽  
Barbara Bonfini ◽  
Annapia Di Gennaro ◽  
Liana Teodori ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Complete Genome ◽  
Central Italy ◽  
Whole Genome ◽  
Genome Sequences ◽  
Abruzzo Region

Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are emerging worldwide. Here, we report the complete genome sequences of 13 severe acute SARS-CoV-2 strains belonging to lineage B.1.525 (variant η).

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