scholarly journals Phylogenetic Analysis of Spike and Envelope Proteins for a Number of Bat Coronaviruses for Understanding the Hypothesis of Possible Origin for the Novel 2019-nCoV

2020 ◽  
pp. 137-144
Author(s):  
Salar Ibrahim Ali
Keyword(s):  
Hong Kong ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Phylogenetic Tree ◽  
Envelope Protein ◽  
Spike Protein ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Close Relationship ◽  
Bat Coronavirus

Coronavirus Disease 19 (COVID-19) emergence reveals  globally a great health issue and due to the limited information and knowledge on the origin of this novel coronavirus 2019 (2019-nCoV). Therefore, this study aims to investigate the evolution and analysis of molecular epidemiology for both Spike and Envelope proteins of 20 available complete genome sequences of different bat coronaviruses including 2019-nCoV in order to find out which type of bat coronaviruses is more likely to be the origin of this new 2019-nCoV and also multiple amino acid sequences of Envelope protein for all bat coronaviruses were aligned for the purpose of finding the greater probability of novel 2019-nCoV original host   among bat coronaviruses. Phylogenetic tree analysis for Spike protein revealed that all 2019-nCoV related coronaviruses isolated from these species of species are discovered in China and Hong Kong and the Middle East bat are less likely to contribute in spreading or to become the origin of 2019-nCoV and all coronaviruses that from Hong Kong and China are located into one clade next to the clade that contains 2019-nCoV coronaviruses which indicates that this group of coronaviruses are genetically different for 2019-nCoV; moreover, Hong Kong and USA bat coronaviruses does not contain the bat coronavirus from China and are located into one clade far from the clade that contains 2019-nCoV indicates that all coronaviruses are genetically very different from 2019-nCoV, and USA bat coronavirus may has no role in generating of 2019-nCoV. The phylogenetic trees analysis of Envelope protein showed that Envelope protein of different coronaviruses are more similar in comparison to Spike protein, USA bat coronavirus has a relatively closeness relationship to 2019-nCoV. Furthermore, Envelope protein alignment showed the closely related amino acid sequence which confirms that the outcomes of phylogenetic tree analysis in which that these bat coronaviruses have genetically close relationship together and more interestingly amino acid sequence (MG772934.1) shows 100% identity with the amino acid sequence of 2019-nCoV (NC 045512.2) and the same virus has a close relationship in both Spike and Envelope due to that in both phylogenetic tree analysis are neighbored with 2019-nCoV in the same clade. 

scholarly journals Phylogenetic Analysis of Kobuvirus and Astrovirus From Korean Wild Boars: 2016-2018

2021 ◽  
Author(s):  
Jihye Shin ◽  
SeEun Choe ◽  
Bang-Hun Hyun ◽  
Dong-Jun An
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Porcine Kobuvirus ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Wild Boars ◽  
Porcine Astrovirus ◽  
The One

Abstract The prevalence of porcine kobuvirus (PKoV) and porcine astrovirus (PAstV) in 845 Korean wild boars (KWB) during 2016-2018 were 28.0% and 10.6%, respectively, and co-infection of two viruses showed 5.1%. Phylogenetic tree analysis also revealed that 236 PKoVs from KWB were divided to diverse lineages within Aichivirus C group but the one strain (WKoV16CN-8627) was included the same cluster with bovine kobuvirus (Achivirus B). Eighty-nine PAstVs from KWB was belonged predominantly to lineage PAstV4 and only one strain (WAst17JN-10931) included novel to lineage PAstV2. Two viruses are epidemic more in young (≤ 12 months) than in old pigs (> 12 months).

Amino acid sequence changes in the haemagglutinin of A/Hong Kong (H3N2) influenza virus during the period 1968–77

Nature ◽  
1980 ◽  
Vol 283 (5746) ◽  
pp. 454-457 ◽  
Author(s):  
W. G. Laver ◽  
G. M. Air ◽  
T. A. Dopheide ◽  
C. W. Ward
Keyword(s):  
Influenza Virus ◽  
Hong Kong ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
H3n2 Influenza ◽  
H3n2 Influenza Virus

scholarly journals Orthology prediction at scalable resolution by phylogenetic tree analysis

2007 ◽  
Vol 8 (1) ◽  
pp. 83 ◽  
Author(s):  
René TJM van der Heijden ◽  
Berend Snel ◽  
Vera van Noort ◽  
Martijn A Huynen
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Orthology Prediction

scholarly journals Phylogenetic Tree Analysis of the Cold-Hot Nature of Traditional Chinese Marine Medicine for Possible Anticancer Activity

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Xianjun Fu ◽  
Xuxia Song ◽  
Xuebo Li ◽  
Kah Keng Wong ◽  
Jiaoyang Li ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Anticancer Activity ◽  
Anticancer Drugs ◽  
Association Rules ◽  
Marine Organisms ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Genus 2 ◽  
Cluster Pattern ◽  
Chinese Marine

Traditional Chinese Marine Medicine (TCMM) represents one of the medicinal resources for research and development of novel anticancer drugs. In this study, to investigate the presence of anticancer activity (AA) displayed by cold or hot nature of TCMM, we analyzed the association relationship and the distribution regularity of TCMMs with different nature (613 TCMMs originated from 1,091 species of marine organisms) via association rules mining and phylogenetic tree analysis. The screened association rules were collected from three taxonomy groups: (1) Bacteria superkingdom, Phaeophyceae class, Fucales order, Sargassaceae family, andSargassumgenus; (2) Viridiplantae kingdom, Streptophyta phylum, Malpighiales class, and Rhizophoraceae family; (3) Holothuroidea class, Aspidochirotida order, andHolothuriagenus. Our analyses showed that TCMMs with closer taxonomic relationship were more likely to possess anticancer bioactivity. We found that the cluster pattern of marine organisms with reported AA tended to cluster with cold nature TCMMs. Moreover, TCMMs with salty-cold nature demonstrated properties for softening hard mass and removing stasis to treat cancers, and species within Metazoa or Viridiplantae kingdom of cold nature were more likely to contain AA properties. We propose that TCMMs from these marine groups may enable focused bioprospecting for discovery of novel anticancer drugs derived from marine bioresources.

scholarly journals Analisis Pohon Filogenik dari Protein Non-Struktural 1 (NS1) Virus Dengue di Kawasan Asia Tenggara

2011 ◽  
Vol 1 (2) ◽  
pp. 69
Author(s):  
Vanny Narita ◽  
Asma Omar ◽  
Agus Masduki
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Dengue Virus ◽  
Protein Sequences ◽  
Amino Acid Sequences ◽  
South East Asia ◽  
Phylogenetic Relation ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Different Strains

<p style="text-align: justify;" align="center">Protein non-struktural 1 adalah protein Virus Dengue yang terkonservasi, tetapi protein non-struktural 1 dari Virus Dengue yang berbeda strain memiliki epitop berbeda yang dapat dikenali oleh sel-B. Epitop-epitop ini mungkin disusun oleh asam amino yang sama dalam urutan yang berbeda. Kemungkinan ini perlu dipertimbangkan dalam rangka memprediksi epitop sekuensial Virus Dengue. Tujuan penelitian kami adalah menganalisis hubungan kekerabatan dan susunan asam amino pada epitop spesifik yang telah dikonfirmasi dari sampel representatif gen protein NS1 dari Virus Dengue di kawasan Asia Tenggara. Hubungan kekerabatan protein non-struktural 1 dianalisis dengan perangkat lunak Lasergene<sup>®</sup>. Sekuen gen ditranslasi terlebih dahulu ke urutan asam amino, dan analisis pohon filogenetik kemudian dilakukan. Hasilnya menunjukkan bahwa hubungan kekerabatan protein non-struktural 1 berkisar antara 72-98%. Selanjutnya, epitop serospesifik dibandingkan berdasarkan hasil pengolahan data dnegan Lasergene. Perbandingan epitop serospesifik menunjukkan bahwa asam amino yang dominan dalam epitop adalah histidin, tirosin, glutamine dan serin</p><h6 style="text-align: center;"><em> </em><em> </em><strong>Abstract</strong></h6>Non-structural 1 protein is a conserved protein of dengue virus, but non-structural 1 proteins of dengue virus from different strains have different epitopes which can be recognized by B-cell. These epitopes may be constructed of similar amino acids in a different arrangement. This possibility  must be considered in order to predict the sequencial epitope of dengue virus. The objective of our study was to analyze the phylogenetic relation and the arrangment of confirmed specific epitopes of dengue strains  from representatives of South East Asia’s NS1 dengue gene samples. The phylogenetic relation of non-structural 1 protein sequences from South East Asia was analyzed with Lasergene<sup>®</sup> software. The gene sequences were translated to amino acid sequences, and phylogenetic tree analysis was performed. The results showed that the relatedness values among full sequences of non-structural 1 protein were 72-98%. Furthermore, the serospesific epitopes were compared according to the Lasergene results. The serospesific epitope comparation showed that the dominant   amino acids in these epitopes were histidine, tyrosine, glutamine and serine.

scholarly journals Prevalence of Human Norovirus by Genotype in Contaminated Groundwater in Korea Over the Last Decade (2007-2016)

2017 ◽  
Author(s):  
Siwon Lee ◽  
Sang-Jung Park ◽  
Ji-Hye Kim ◽  
Wonseok Lee ◽  
Hyen-Mi Chung
Keyword(s):  
Phylogenetic Tree ◽  
Republic Of Korea ◽  
Contaminated Groundwater ◽  
Human Norovirus ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Groundwater Samples ◽  
Reference Sequences ◽  
Groundwater Wells

This study investigated the presence of human Norovirus (HuNoV) by genotype in 1,486 groundwater samples, collected from 843 groundwater wells suspected of contamination during 2007-2016, in Republic of Korea. We identified and genotyped 186 HuNoV sequences in 178 HuNoV-positive samples using the RIVM-NoroNet norovirus genotyping tool (NGT) and phylogenetic tree analysis based on RIVM-NoroNet reference sequences. HuNoV GII was more prevalent than GI. The major genotypes detected were HuNoV GII.4 (43.0%), GII.22 (15.6%), GI.5 (10.2%) and GI.1 (8.6%); 14 genotypes accounted for &lt; 5.0%. Increasing HuNoV GII.17 has displayed a worldwide trend, including in Europe and Asia since 2010, and it was the dominant HuNoV genotype during 2013-2014 in Korea. However, HuNoV GII.4 was the major genotype detected in groundwater in Korea in 2015-2016, and it is becoming increasingly prevalent similar to HuNoV GII.17.

scholarly journals Molecular identification and genotyping of Atopobium vaginae, 16s rRNA gene from Bacterial Vaginosis miscarriage women in AL-Hillah city

2013 ◽  
Vol 11 (01) ◽  
pp. 74-82
Author(s):  
Ilham A. Bunyan ◽  
Asmaa K. Gatea ◽  
Alaa K. Hameed
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Tree ◽  
Rrna Gene ◽  
City Hospital ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Columbia Blood Agar ◽  
The 16S Rrna Gene ◽  
Atopobium Vaginae

This study was aimed to determine the Atopobium vaginae associated BV in vaginosis women and women with miscarriage. Also other aim, the DNA sequencing was performed for phylogenetic tree analysis of 16SrRNA gene in local Atopobium vaginae isolates in comparison with NCBI-Genbank global Atopobium vaginae isolates and finally submission of the present isolates in NCBI-Genbank database. One hundred fifty (150) high vaginal swabs were collected from women with vaginosis(Seventy five samples were taken from married vaginosis women without miscarriage and Seventy five samples from vaginosis women with miscarriage) from Babylon city hospital and private clinics. The age of patient (15– 45) years. The sample was collected by disposable swabs, genomic DNA was extracted from these swabs. 16s rRNA gene detection by polymerase chain reaction technique . Atopobium vaginae was isolated on Columbia blood agar supplemented with antibiotic for the first time in Iraq, the study confirmed that 9 (12.00%) and 5(6.66%) of Atopobium vaginae out of 150 swabs isolated from miscarriage and non-miscarriage vaginosis women respectively. According to the detection of the 16S rRNA gene, the study revealed that 69(92.00%)and 47(62.66%)of Atopobium vaginae out of 150 swabs obtained from miscarriage and non-miscarriage vaginosis women respectively. BLAST analysis showed that the 16S rRNA gene shared more than 98- 99% sequence compatibility with the sequences of Atopobium vaginae. Furthermore, the phylogenetic tree analysis of the 16S rRNA gene indicated that local Atopobium vaginae (NO.1 and NO. 2 ) isolates shared higher homology with other Atopobium vaginae isolates available in the GenBank. The homology of the nucleotides was between (99.17% and 98.75%) respectively.

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