scholarly journals Whole-genome analysis reveals the complex evolutionary dynamics of Kenyan G2P[4] human rotavirus strains

2011 ◽  
Vol 92 (9) ◽  
pp. 2201-2208 ◽  
Author(s):  
Souvik Ghosh ◽  
Noriaki Adachi ◽  
Zipporah Gatheru ◽  
James Nyangao ◽  
Dai Yamamoto ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Complete Genome ◽  
Evolutionary Dynamics ◽  
Genomic Analysis ◽  
Whole Genome ◽  
Genome Sequences ◽  
Whole Genome Analysis ◽  
Human Rotavirus ◽  
Genotype Constellation ◽  
Common Causes

Although G2P[4] rotaviruses are common causes of acute childhood diarrhoea in Africa, to date there are no reports on whole genomic analysis of African G2P[4] strains. In this study, the nearly complete genome sequences of two Kenyan G2P[4] strains, AK26 and D205, detected in 1982 and 1989, respectively, were analysed. Strain D205 exhibited a DS-1-like genotype constellation, whilst strain AK26 appeared to be an intergenogroup reassortant with a Wa-like NSP2 genotype on the DS-1-like genotype constellation. The VP2-4, VP6-7, NSP1, NSP3 and NSP5 genes of strain AK26 and the VP2, VP4, VP7 and NSP1–5 genes of strain D205 were closely related to those of the prototype or other human G2P[4] strains. In contrast, their remaining genes were distantly related, and, except for NSP2 of AK26, appeared to originate from or share a common origin with rotavirus genes of artiodactyl (ruminant and camelid) origin. These observations highlight the complex evolutionary dynamics of African G2P[4] rotaviruses.

scholarly journals Complete Genome Sequence of the Yogurt Isolate Lactobacillus delbrueckii subsp. bulgaricus ACA-DC 87

2017 ◽  
Vol 5 (34) ◽  
Author(s):  
Voula Alexandraki ◽  
Maria Kazou ◽  
Bruno Pot ◽  
Effie Tsakalidou ◽  
Konstantinos Papadimitriou
Keyword(s):  
Genome Sequence ◽  
Genome Analysis ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Lactobacillus Delbrueckii ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Content Type ◽  
Lactobacillus Delbrueckii Subsp

ABSTRACT Lactobacillus delbrueckii subsp. bulgaricus is widely used in the production of yogurt and cheese. In this study, we present the complete genome sequence of L. delbrueckii subsp. bulgaricus ACA-DC 87 isolated from traditional Greek yogurt. Whole-genome analysis may reveal desirable technological traits of the strain for dairy fermentations.

scholarly journals Evolutionary Dynamics of Local Pandemic H1N1/2009 Influenza Virus Lineages Revealed by Whole-Genome Analysis

2011 ◽  
Vol 86 (1) ◽  
pp. 11-18 ◽  
Author(s):  
G. J. Baillie ◽  
M. Galiano ◽  
P.-M. Agapow ◽  
R. Myers ◽  
R. Chiam ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Genome Analysis ◽  
Evolutionary Dynamics ◽  
Whole Genome ◽  
Pandemic H1n1 ◽  
Whole Genome Analysis ◽  
Pandemic H1n1 2009

scholarly journals Complete Genome Sequence of the Sourdough Isolate Lactobacillus zymae ACA-DC 3411

2017 ◽  
Vol 5 (30) ◽  
Author(s):  
Maria Kazou ◽  
Voula Alexandraki ◽  
Bruno Pot ◽  
Effie Tsakalidou ◽  
Konstantinos Papadimitriou
Keyword(s):  
Lactic Acid ◽  
Genome Sequence ◽  
Genome Analysis ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Lactobacillus Brevis ◽  
Whole Genome ◽  
Adaptive Traits ◽  
Whole Genome Analysis ◽  
Content Type

ABSTRACT Lactobacillus zymae is a Gram-positive lactic acid bacterium belonging to the Lactobacillus brevis clade. Here, we report the first complete genome sequence of L. zymae ACA-DC 3411, which was isolated from traditional Greek wheat sourdough. Whole-genome analysis may reveal adaptive traits of strain ACA-DC 3411 in the sourdough ecosystem.

scholarly journals GAAP: A Genome Assembly + Annotation Pipeline

2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Jinhwa Kong ◽  
Sun Huh ◽  
Jung-Im Won ◽  
Jeehee Yoon ◽  
Baeksop Kim ◽  
...  
Keyword(s):  
Genome Analysis ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Genomic Analysis ◽  
Whole Genome ◽  
High Throughput Analysis ◽  
Whole Genome Analysis ◽  
A Genome ◽  
Base Sequences ◽  
Wide Range

Genomic analysis begins with de novo assembly of short-read fragments in order to reconstruct full-length base sequences without exploiting a reference genome sequence. Then, in the annotation step, gene locations are identified within the base sequences, and the structures and functions of these genes are determined. Recently, a wide range of powerful tools have been developed and published for whole-genome analysis, enabling even individual researchers in small laboratories to perform whole-genome analyses on their objects of interest. However, these analytical tools are generally complex and use diverse algorithms, parameter setting methods, and input formats; thus, it remains difficult for individual researchers to select, utilize, and combine these tools to obtain their final results. To resolve these issues, we have developed a genome analysis pipeline (GAAP) for semiautomated, iterative, and high-throughput analysis of whole-genome data. This pipeline is designed to perform read correction, de novo genome (transcriptome) assembly, gene prediction, and functional annotation using a range of proven tools and databases. We aim to assist non-IT researchers by describing each stage of analysis in detail and discussing current approaches. We also provide practical advice on how to access and use the bioinformatics tools and databases and how to implement the provided suggestions. Whole-genome analysis of Toxocara canis is used as case study to show intermediate results at each stage, demonstrating the practicality of the proposed method.

scholarly journals Whole Genome Analysis of African G12P[6] and G12P[8] Rotaviruses Provides Evidence of Porcine-Human Reassortment at NSP2, NSP3, and NSP4

2021 ◽  
Vol 11 ◽  
Author(s):  
Fortunate Mokoena ◽  
Mathew Dioh Esona ◽  
Luyanda Mapaseka Seheri ◽  
Martin Munene Nyaga ◽  
Nonkululelo Bonakele Magagula ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Sub Saharan Africa ◽  
Interspecies Transmission ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Eastern Ethiopia ◽  
Single Strain ◽  
Ion Torrent Pgm ◽  
Genotype Constellation ◽  
Genotype 2

Group A rotaviruses (RVA) represent the most common cause of pediatric gastroenteritis in children <5 years, worldwide. There has been an increase in global detection and reported cases of acute gastroenteritis caused by RVA genotype G12 strains, particularly in Africa. This study sought to characterize the genomic relationship between African G12 strains and determine the possible origin of these strains. Whole genome sequencing of 34 RVA G12P[6] and G12P[8] strains detected from the continent including southern (South Africa, Zambia, Zimbabwe), eastern (Ethiopia, Uganda), central (Cameroon), and western (Togo) African regions, were sequenced using the Ion Torrent PGM method. The majority of the strains possessed a Wa-like backbone with consensus genotype constellation of G12-P[6]/P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1, while a single strain from Ethiopia displayed a DS-1-like genetic constellation of G12-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. In addition, three Ethiopian and one South African strains exhibited a genotype 2 reassortment of the NSP3 gene, with genetic constellation of G12-P[8]-I1-R1-C1-M1-A1-N1-T2-E1-H1. Overall, 10 gene segments (VP1–VP4, VP6, and NSP1–NSP5) of African G12 strains were determined to be genetically related to cognate gene sequences from globally circulating human Wa-like G12, G9, and G1 strains with nucleotide (amino acid) identities in the range of 94.1–99.9% (96.5–100%), 88.5–98.5% (93–99.1%), and 89.8–99.0% (88.7–100%), respectively. Phylogenetic analysis showed that the Ethiopian G12P[6] possessing a DS-1-like backbone consistently clustered with G2P[4] strains from Senegal and G3P[6] from Ethiopia with the VP1, VP2, VP6, and NSP1–NSP4 genes. Notably, the NSP2, NSP3, and NSP4 of most of the study strains exhibited the closest relationship with porcine strains suggesting the occurrence of reassortment between human and porcine strains. Our results add to the understanding of potential roles that interspecies transmission play in generating human rotavirus diversity through reassortment events and provide insights into the evolutionary dynamics of G12 strains spreading across selected sub-Saharan Africa regions.

scholarly journals Whole-Genome Analyses Identifies Multiple Reassortant Rotavirus Strains in Rwanda Post-Vaccine Introduction

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 95
Author(s):  
Sebotsana Rasebotsa ◽  
Jeannine Uwimana ◽  
Milton T. Mogotsi ◽  
Kebareng Rakau ◽  
Nonkululeko B. Magagula ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genome Analysis ◽  
Evolutionary Dynamics ◽  
Developed Countries ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Evolutionary Mechanisms ◽  
Vaccine Introduction ◽  
Rotavirus Vaccines ◽  
The Impact

Children in low-and middle-income countries, including Rwanda, experience a greater burden of rotavirus disease relative to developed countries. Evolutionary mechanisms leading to multiple reassortant rotavirus strains have been documented over time which influence the diversity and evolutionary dynamics of novel rotaviruses. Comprehensive rotavirus whole-genome analysis was conducted on 158 rotavirus group A (RVA) samples collected pre- and post-vaccine introduction in children less than five years in Rwanda. Of these RVA positive samples, five strains with the genotype constellations G4P[4]-I1-R2-C2-M2-A2-N2-T1-E1-H2 (n = 1), G9P[4]-I1-R2-C2-M2-A1-N1-T1-E1-H1 (n = 1), G12P[8]-I1-R2-C2-M1-A1-N2-T1-E2-H3 (n = 2) and G12P[8]-I1-R1-C1-M1-A2-N2-T2-E1-H1 (n = 1), with double and triple gene reassortant rotavirus strains were identified. Phylogenetic analysis revealed a close relationship between the Rwandan strains and cognate human RVA strains as well as the RotaTeq® vaccine strains in the VP1, VP2, NSP2, NSP4 and NSP5 gene segments. Pairwise analyses revealed multiple differences in amino acid residues of the VP7 and VP4 antigenic regions of the RotaTeq® vaccine strain and representative Rwandan study strains. Although the impact of such amino acid changes on the effectiveness of rotavirus vaccines has not been fully explored, this analysis underlines the potential of rotavirus whole-genome analysis by enhancing knowledge and understanding of intergenogroup reassortant strains circulating in Rwanda post vaccine introduction.

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