Faculty Opinions recommendation of Microbial species delineation using whole genome sequences.

We report 17 draft genomes for 14 unidentified Veillonella sp. strains closely related in 16S rRNA gene-based phylogeny and type strains of 3 Veillonella species with the aims of deciphering relationships between related species, evaluating the accuracy of current thresholds for species delineation, and robustly describing new species in the genus.

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Faculty Opinions recommendation of Inference of human population history from individual whole-genome sequences.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.11961958.13084059 ◽

2011 ◽

Author(s):

Stephen Wright

Keyword(s):

Human Population ◽

Population History ◽

Whole Genome ◽

Genome Sequences

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Mitochondrial DNA mutations in papuan humans: characterization of whole genome sequences and its application for susceptibility to disease

International Journal of Pharma and Bio Sciences ◽

10.22376/ijpbs.2019.10.2.b108-112 ◽

2019 ◽

Vol 10 (2) ◽

Author(s):

YOHANIS NGILI ◽

ROSYE H.R. TANJUNG

Keyword(s):

Mitochondrial Dna ◽

Whole Genome ◽

Genome Sequences ◽

Mitochondrial Dna Mutations ◽

Dna Mutations

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Molecular Epidemiology and Whole-Genome Analysis of Bovine Foamy Virus in Japan

Viruses ◽

10.3390/v13061017 ◽

2021 ◽

Vol 13 (6) ◽

pp. 1017

Author(s):

Hirohisa Mekata ◽

Tomohiro Okagawa ◽

Satoru Konnai ◽

Takayuki Miyazawa

Keyword(s):

Phylogenetic Analyses ◽

Foamy Virus ◽

Pcr Analysis ◽

Whole Genome ◽

Genome Sequences ◽

Whole Genome Analysis ◽

Virus Family ◽

Bovine Foamy Virus ◽

Novel Genotype

Bovine foamy virus (BFV) is a member of the foamy virus family in cattle. Information on the epidemiology, transmission routes, and whole-genome sequences of BFV is still limited. To understand the characteristics of BFV, this study included a molecular survey in Japan and the determination of the whole-genome sequences of 30 BFV isolates. A total of 30 (3.4%, 30/884) cattle were infected with BFV according to PCR analysis. Cattle less than 48 months old were scarcely infected with this virus, and older animals had a significantly higher rate of infection. To reveal the possibility of vertical transmission, we additionally surveyed 77 pairs of dams and 3-month-old calves in a farm already confirmed to have BFV. We confirmed that one of the calves born from a dam with BFV was infected. Phylogenetic analyses revealed that a novel genotype was spread in Japan. In conclusion, the prevalence of BFV in Japan is relatively low and three genotypes, including a novel genotype, are spread in Japan.

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

Scientific Reports ◽

10.1038/s41598-021-89361-7 ◽

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.

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Comparison of whole genome sequences of three Bacillus cereus strains reveals the food safety risks of Apostichopus japonicus in China

Aquaculture Reports ◽

10.1016/j.aqrep.2021.100649 ◽

2021 ◽

Vol 20 ◽

pp. 100649

Author(s):

Xiaoran Zhao ◽

Ruijun Li ◽

Huifeng Dang ◽

Luo Wang ◽

Songzhe Fu ◽

...

Keyword(s):

Food Safety ◽

Bacillus Cereus ◽

Apostichopus Japonicus ◽

Whole Genome ◽

Genome Sequences ◽

Safety Risks

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Whole-Genome Sequences of Influenza A(H1N1)pdm09 Virus Isolates from Kerala, India

Genome Announcements ◽

10.1128/genomea.00598-17 ◽

2017 ◽

Vol 5 (28) ◽

Cited By ~ 1

Author(s):

Sara Jones ◽

Raji Prasad ◽

Anjana S. Nair ◽

Sanjai Dharmaseelan ◽

Remya Usha ◽

...

Keyword(s):

Amino Acid ◽

Amino Acid Analysis ◽

Influenza A ◽

Whole Genome Sequence ◽

Whole Genome ◽

H1n1 Pandemic ◽

Genome Sequences ◽

Influenza A H1n1 ◽

Virus Isolates ◽

New Mutations

ABSTRACT We report here the whole-genome sequence of six clinical isolates of influenza A(H1N1)pdm09, isolated from Kerala, India. Amino acid analysis of all gene segments from the A(H1N1)pdm09 isolates obtained in 2014 and 2015 identified several new mutations compared to the 2009 A(H1N1) pandemic strain.

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Comparison of Whole-Genome Sequences from Two Colony Morphovars of Burkholderia pseudomallei

Genome Announcements ◽

10.1128/genomea.01194-15 ◽

2015 ◽

Vol 3 (5) ◽

Cited By ~ 6

Author(s):

Pei-Tan Hsueh ◽

Yao-Shen Chen ◽

Hsi-Hsu Lin ◽

Pei-Ju Liu ◽

Wen-Fan Ni ◽

...

Keyword(s):

Burkholderia Pseudomallei ◽

Repeated Sequences ◽

Whole Genome ◽

Genome Sequences ◽

Single Base

The entire genomes of two isogenic morphovars (vgh16W and vgh16R) of Burkholderia pseudomallei were sequenced. A comparison of the sequences from both strains indicates that they show 99.99% identity, are composed of 22 tandem repeated sequences with <100 bp of indels, and have 199 single-base variants.

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