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 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 Finished Whole-Genome Sequences of Two Clostridium botulinum Type A(B) Isolates

2017 ◽  
Vol 5 (21) ◽  
Author(s):  
Jessica L. Halpin ◽  
Karen Hill ◽  
Shannon L. Johnson ◽  
David Carlton Bruce ◽  
T. Brian Shirey ◽  
...  
Keyword(s):  
United States ◽  
Clostridium Botulinum ◽  
Type A ◽  
The United States ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Botulinum Type ◽  
Clinically Significant

ABSTRACT Clostridium botulinum secretes a potent neurotoxin that causes devastating effects when ingested, including paralysis and death if not treated. In the United States, some clinically significant strains produce toxin type A while also harboring a silent B gene. These are the first two closed genome sequences published for this subset.

scholarly journals Draft Genome Sequences of Two Salmonella enterica Strains Isolated from Sprouted Chia and Flax Seed Powders

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Jennifer Ronholm ◽  
Nicholas Petronella ◽  
Sandeep Tamber
Keyword(s):  
United States ◽  
Salmonella Enterica ◽  
Draft Genome ◽  
The United States ◽  
Whole Genome ◽  
Flax Seed ◽  
Genome Sequences ◽  
Chia Seed ◽  
First Time

A 2014 foodborne salmonellosis outbreak in Canada and the United States implicated, for the first time, sprouted chia seed powder as the vehicle of transmission. Here, we report the draft whole genome sequences of two Salmonella enterica strains isolated from sprouted powders related to the aforementioned outbreak.

scholarly journals Genome Sequences of Mycobacterium Strains Recovered from Captive Elephants with Tuberculosis

2021 ◽  
Vol 10 (36) ◽  
Author(s):  
Evan P. Brenner ◽  
Syeda A. Hadi ◽  
Beth Harris ◽  
Suelee Robbe-Austerman ◽  
Srinand Sreevatsan
Keyword(s):  
United States ◽  
Mycobacterium Tuberculosis ◽  
Endangered Species ◽  
Human Health ◽  
The United States ◽  
Whole Genome ◽  
Genome Sequences ◽  
Asian Elephants ◽  
Content Type

Members of the Mycobacterium tuberculosis complex cause tuberculosis, infamous for enormous impacts on human health. As zoonoses, they also threaten endangered species like African/Asian elephants. We report the whole-genome sequences of Mycobacterium tuberculosis biovars tuberculosis and bovis from two zoo elephants in the United States.

scholarly journals Complete Genome Sequences of Three Fish-Associated Streptococcus agalactiae Isolates

2018 ◽  
Vol 6 (6) ◽  
pp. e00025-18 ◽  
Author(s):  
Anita Jaglarz ◽  
Artur Gurgul ◽  
William J. Leigh ◽  
Janina Z. Costa ◽  
Kim D. Thompson
Keyword(s):  
United States ◽  
Costa Rica ◽  
Streptococcus Agalactiae ◽  
Oreochromis Niloticus ◽  
Complete Genome ◽  
The United States ◽  
Whole Genome ◽  
Genome Sequences ◽  
Group B

ABSTRACTThe whole-genome sequences are described here for three group B Streptococcus (GBS) (S. agalactiae) serotype Ib isolates obtained from tilapia (Oreochromis niloticus) farmed at sites in Honduras, Costa Rica, and the United States. The bacteria were isolated from the brains of fish displaying signs of streptococcosis.

scholarly journals High-Quality Whole-Genome Sequences for 21 Enterotoxigenic Escherichia coli Strains Generated with PacBio Sequencing

2018 ◽  
Vol 6 (2) ◽  
Author(s):  
Peyton Smith ◽  
Rebecca L. Lindsey ◽  
Lori A. Rowe ◽  
Dhwani Batra ◽  
Devon Stripling ◽  
...  
Keyword(s):  
United States ◽  
Escherichia Coli ◽  
The United States ◽  
Enterotoxigenic Escherichia Coli ◽  
Whole Genome ◽  
Cruise Ship ◽  
Genome Sequences ◽  
Pacbio Sequencing ◽  
High Quality ◽  
Surveillance Studies

ABSTRACT Enterotoxigenic Escherichia coli (ETEC) is an important diarrheagenic pathogen. We report here the high-quality whole-genome sequences of 21 ETEC strains isolated from patients in the United States, international diarrheal surveillance studies, and cruise ship outbreaks.

scholarly journals Comparison of Outer Membrane Protein Genesompandpmpin the Whole Genome Sequences ofChlamydia pneumoniaeIsolates from Japan and the United States

2000 ◽  
Vol 181 (s3) ◽  
pp. S524-S527 ◽  
Author(s):  
Mutsunori Shirai ◽  
Hideki Hirakawa ◽  
Kazunobu Ouchi ◽  
Mitsuaki Tabuchi ◽  
Fumio Kishi ◽  
...  
Keyword(s):  
United States ◽  
Membrane Protein ◽  
Outer Membrane ◽  
Outer Membrane Protein ◽  
The United States ◽  
Whole Genome ◽  
Genome Sequences

scholarly journals Draft Genome Sequences of Nine Vibrio sp. Isolates from across the United States Closely Related to Vibrio cholerae

2018 ◽  
Vol 7 (21) ◽  
Author(s):  
Mohammad Tarequl Islam ◽  
Kevin Liang ◽  
Monica S. Im ◽  
Jonathan Winkjer ◽  
Shelby Busby ◽  
...  
Keyword(s):  
United States ◽  
Vibrio Cholerae ◽  
Draft Genome ◽  
The United States ◽  
Whole Genome ◽  
Human Pathogen ◽  
Genome Sequences ◽  
Content Type

We are reporting whole-genome sequences of nine Vibrio sp. isolates closely related to the waterborne human pathogen Vibrio cholerae.

scholarly journals Two SARS-CoV-2 Genome Sequences of Isolates from Rural U.S. Patients Harboring the D614G Mutation, Obtained Using Nanopore Sequencing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Piroon Jenjaroenpun ◽  
Visanu Wanchai ◽  
Kikumi D. Ono-Moore ◽  
Jennifer Laudadio ◽  
Laura P. James ◽  
...  
Keyword(s):  
United States ◽  
Severe Acute Respiratory Syndrome ◽  
Viral Genome ◽  
The United States ◽  
Network Protocol ◽  
Nanopore Sequencing ◽  
Genome Sequences ◽  
Oxford Nanopore ◽  
Complete Sequences ◽  
Oxford Nanopore Technologies

ABSTRACT Two coding-complete sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were obtained from samples from two patients in Arkansas, in the southeastern corner of the United States. The viral genome was obtained using the ARTIC Network protocol and Oxford Nanopore Technologies sequencing.

scholarly journals Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan

2021 ◽  
Vol 17 (6) ◽  
pp. e1009619
Author(s):  
Yosuke Hirotsu ◽  
Masao Omata
Keyword(s):  
United States ◽  
Severe Acute Respiratory Syndrome ◽  
The United States ◽  
Spike Protein ◽  
Taqman Assay ◽  
Receptor Binding Domain ◽  
Genome Sequences ◽  
Protein Receptor ◽  
History Of ◽  
Global Initiative

We aimed to investigate novel emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages in Japan that harbor variants in the spike protein receptor-binding domain (RBD). The total nucleic acid contents of samples from 159 patients with coronavirus disease 2019 (COVID-19) were subjected to whole genome sequencing. The SARS-CoV-2 genome sequences from these patients were examined for variants in spike protein RBD. In January 2021, three family members (one aged in their 40s and two aged under 10 years old) were found to be infected with SARS-CoV-2 harboring W152L/E484K/G769V mutations. These three patients were living in Japan and had no history of traveling abroad. After identifying these cases, we developed a TaqMan assay to screen for the above hallmark mutations and identified an additional 14 patients with the same mutations. The associated virus strain was classified into the GR clade (Global Initiative on Sharing Avian Influenza Data [GISAID]), 20B clade (Nextstrain), and R.1 lineage (Phylogenetic Assignment of Named Global Outbreak [PANGO] Lineages). As of April 22, 2021, R.1 lineage SARS-CoV-2 has been identified in 2,388 SARS-CoV-2 entries in the GISAID database, many of which were from Japan (38.2%; 913/2,388) and the United States (47.1%; 1,125/2,388). Compared with that in the United States, the percentage of SARS-CoV-2 isolates belonging to the R.1 lineage in Japan increased more rapidly over the period from October 24, 2020 to April 18, 2021. R.1 lineage SARS-CoV-2 has potential escape mutations in the spike protein RBD (E484K) and N-terminal domain (W152L); therefore, it will be necessary to continue to monitor the R.1 lineage as it spreads around the world.

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