scholarly journals Phylogenetic relationships of endornaviruses in common bean from the western highlands of Kenya and global sequences

2018 ◽  
Author(s):  
James M Wainaina ◽  
Elijah Ateka ◽  
Timothy Makori ◽  
Monica A Kehoe ◽  
Laura M Boykin
Keyword(s):  
Phaseolus Vulgaris ◽  
Complete Genome ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Current Knowledge ◽  
Sequence Similarity ◽  
Evolutionary Relationship ◽  
Sub Saharan Africa ◽  
Complete Genomes ◽  
Sub Saharan

Background: Endornaviruses are non-pathogenic viruses infecting multiple agricultural important crops including legumes, with global distribution. However, there is an absence on the complete genome of endornaviruses from legumes in particular with the sub-Saharan region. In this study, we report the first complete genomes of PvEV1 and PvEV2, and the evolutionary relationship of these genomes. Methods: Viral symptomatic common beans (Phaseolus vulgaris) showing Bean common mosaic necrosis virus (BCMNV) symptoms from Vihiga county, in the western highlands of Kenya were collected during field survey’s in the region. High throughput sequencing (RNA-Seq) was carried out on total RNA isolated from symptomatic leaf samples. Subsequently, de novo assembly and reference mapping was carried out to obtain the complete genomes of PvEV-1 and PvEV-2. Results: We identified the complete genome of Phaseolus vulgaris endornavirus 1 and 2 (PvEV-1 and PvEV-2) from sub-Saharan Africa (SSA). The average genome size of PvEV-1 was ~13,890 nucleotides (nt) while PvEV-2 was ~14,698 nt, encoding a single open reading frame (ORF). Single ORFs ranged from 4,632 to 4,633 aa in PvEV-1 and from 4,899 – to 4,954 aa in PvEV-2. Both ORFs encoded for the RNA-dependent RNA polymerase (RdRP) gene. The percentage sequence similarity between PvEV-1, PvEV-2 from this study GenBanks sequences was 29 % to 99 %. Bayesian phylogenetic analysis resolved in two well-supported monophyletic clades, with isolates from this study clustering with those from Brazil sequences. Discussion: This study provides the first insights into the evolutionary relationships of PvEV from SSA diverse and contributes towards filling the current knowledge gaps on endornaviruses

scholarly journals Phylogenetic relationships of endornaviruses in common bean from the western highlands of Kenya and global sequences

2018 ◽  
Author(s):  
James M Wainaina ◽  
Elijah Ateka ◽  
Timothy Makori ◽  
Monica A Kehoe ◽  
Laura M Boykin
Keyword(s):  
Phaseolus Vulgaris ◽  
Complete Genome ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Current Knowledge ◽  
Sequence Similarity ◽  
Evolutionary Relationship ◽  
Sub Saharan Africa ◽  
Complete Genomes ◽  
Sub Saharan

Background: Endornaviruses are non-pathogenic viruses infecting multiple agricultural important crops including legumes, with global distribution. However, there is an absence on the complete genome of endornaviruses from legumes in particular with the sub-Saharan region. In this study, we report the first complete genomes of PvEV1 and PvEV2, and the evolutionary relationship of these genomes. Methods: Viral symptomatic common beans (Phaseolus vulgaris) showing Bean common mosaic necrosis virus (BCMNV) symptoms from Vihiga county, in the western highlands of Kenya were collected during field survey’s in the region. High throughput sequencing (RNA-Seq) was carried out on total RNA isolated from symptomatic leaf samples. Subsequently, de novo assembly and reference mapping was carried out to obtain the complete genomes of PvEV-1 and PvEV-2. Results: We identified the complete genome of Phaseolus vulgaris endornavirus 1 and 2 (PvEV-1 and PvEV-2) from sub-Saharan Africa (SSA). The average genome size of PvEV-1 was ~13,890 nucleotides (nt) while PvEV-2 was ~14,698 nt, encoding a single open reading frame (ORF). Single ORFs ranged from 4,632 to 4,633 aa in PvEV-1 and from 4,899 – to 4,954 aa in PvEV-2. Both ORFs encoded for the RNA-dependent RNA polymerase (RdRP) gene. The percentage sequence similarity between PvEV-1, PvEV-2 from this study GenBanks sequences was 29 % to 99 %. Bayesian phylogenetic analysis resolved in two well-supported monophyletic clades, with isolates from this study clustering with those from Brazil sequences. Discussion: This study provides the first insights into the evolutionary relationships of PvEV from SSA diverse and contributes towards filling the current knowledge gaps on endornaviruses

scholarly journals Transmission of SARS-CoV-2 in Northern Ghana; Insights from Whole Genome Sequencing

2020 ◽  
Author(s):  
Augustina Angelina Sylverken ◽  
Philip El-Duah ◽  
Michael Owusu ◽  
Julia Schneider ◽  
Richmond Yeboah ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Viral Rna ◽  
Sub Saharan Africa ◽  
Northern Ghana ◽  
Long Distance ◽  
Foreign Travel ◽  
Two Samples ◽  
Complete Genomes ◽  
History Of ◽  
Sub Saharan

In regions lacking genomic data, analysis of sequences from the early stages of an outbreak can provide important insights into the diversity of pathogens present. Following the detection of the first imported case of COVID-19 in the Northern sector of Ghana on 13th March 2020, we have now molecularly characterized and phylogenetically analysed sequences including three (3) complete genomes of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) isolated from nine (9) patients observed in Ghana. Eight (8) of these patients reported with a recent history of foreign travel and one (1) with no history of foreign travel. We performed high throughput sequencing for 9 samples following the determination of high concentration of viral RNA. In addition, we estimated the potential impact that long distance transportation of samples to testing centres may have on sequencing outcomes. Here, two samples that were closest in terms of viral RNA concentration but transported from sites which are over 400km apart were assessed. All sequences were compared to previous sequences from Ghana and representative sequences from regions where our patients had previously travelled. Complete genomes were obtained for three (3) sequences and with another near complete genome with a coverage of 95.6%. Sequences with coverage in excess of 80% were found to belong to three lineages namely A, B.1 and B.2. Our sequences clustered in two different clades with the majority falling within a clade composed of sequences from sub-Saharan Africa. Less RNA fragmentation was seen in sample KATH23 which was collected 9km compared with sample TTH6 which was collected and transported over a distance of 400km to the testing site. The clustering of several sequences from sub-Saharan Africa suggests regional circulation of the viruses in the subregion. Importantly, there may be the need to decentralize testing sites and build more capacity across Africa to boost the sequencing output of the subregion.

scholarly journals Complete Genome Sequence of a Hepatitis E Virus Genotype 1e Strain from an Outbreak in Nigeria, 2017

2019 ◽  
Vol 8 (1) ◽  
Author(s):  
Olusola Anuoluwapo Akanbi ◽  
Dominik Harms ◽  
Bo Wang ◽  
Oluyinka Oladele Opaleye ◽  
Olufisayo Adesina ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Hepatitis E Virus ◽  
Hepatitis E ◽  
Sub Saharan Africa ◽  
Genotype 1 ◽  
Virus Genotype ◽  
Sub Saharan

Hepatitis E virus genotype 1 (HEV-1) is associated with large epidemics. Notably, HEV subtype 1e (HEV-1e) has caused HEV outbreaks in sub-Saharan Africa.

scholarly journals Management of chronic respiratory complications in children and adolescents with sickle cell disease

2020 ◽  
Vol 29 (157) ◽  
pp. 200054
Author(s):  
Michele Arigliani ◽  
Atul Gupta
Keyword(s):  
Sickle Cell Disease ◽  
Sickle Cell ◽  
Current Knowledge ◽  
Sub Saharan Africa ◽  
Cell Disease ◽  
Respiratory Complications ◽  
Progressive Decline ◽  
Blood Disorder ◽  
Life Threatening ◽  
Sub Saharan

Sickle cell disease (SCD) is a life-threatening hereditary blood disorder that affects millions of people worldwide, especially in sub-Saharan Africa. This condition has a multi-organ involvement and highly vascularised organs, such as the lungs, are particularly affected. Chronic respiratory complications of SCD involve pulmonary vascular, parenchymal and airways alterations. A progressive decline of lung function often begins in childhood. Asthma, sleep-disordered breathing and chronic hypoxaemia are common and associated with increased morbidity. Pulmonary hypertension is a serious complication, more common in adults than in children. Although there is a growing attention towards respiratory care of patients with SCD, evidence regarding the prognostic meaning and optimal management of pulmonary issues in children with this condition is limited.This narrative review presents state-of-the-art evidence regarding the epidemiology, pathophysiology and therapeutic options for chronic respiratory complications commonly seen in paediatric patients with SCD. Furthermore, it highlights the gaps in the current knowledge and indicates future directions for studies that aim to improve our understanding of chronic respiratory complications in children with SCD.

scholarly journals Molecular Characterisation of a Novel and Highly Divergent Passerine Adenovirus 1

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 1036
Author(s):  
Ajani Athukorala ◽  
Jade K. Forwood ◽  
David N. Phalen ◽  
Subir Sarker
Keyword(s):  
Complete Genome ◽  
Sequence Similarity ◽  
Evolutionary Relationship ◽  
Passerine Bird ◽  
The Novel ◽  
Transmembrane Helices ◽  
Novel Genes ◽  
Separate Species ◽  
Natural Host Species ◽  
Genes Encoding

Wild birds harbour a large number of adenoviruses that remain uncharacterised with respect to their genomic organisation, diversity, and evolution within complex ecosystems. Here, we present the first complete genome sequence of an atadenovirus from a passerine bird that is tentatively named Passerine adenovirus 1 (PaAdV-1). The PaAdV-1 genome is 39,664 bp in length, which was the longest atadenovirus to be sequenced, to the best of our knowledge, and contained 42 putative genes. Its genome organisation was characteristic of the members of genus Atadenovirus; however, the novel PaAdV-1 genome was highly divergent and showed the highest sequence similarity with psittacine adenovirus-3 (55.58%). Importantly, PaAdV-1 complete genome was deemed to contain 17 predicted novel genes that were not present in any other adenoviruses sequenced to date, with several of these predicted novel genes encoding proteins that harbour transmembrane helices. Subsequent analysis of the novel PaAdV-1 genome positioned phylogenetically to a distinct sub-clade with all others sequenced atadenoviruses and did not show any obvious close evolutionary relationship. This study concluded that the PaAdV-1 complete genome described here is not closely related to any other adenovirus isolated from avian or other natural host species and that it should be considered a separate species.

scholarly journals Arthritogenic Alphaviruses: A Worldwide Emerging Threat?

2019 ◽  
Vol 7 (5) ◽  
pp. 133 ◽  
Author(s):  
Laura I. Levi ◽  
Marco Vignuzzi
Keyword(s):  
Chikungunya Virus ◽  
Neglected Tropical Diseases ◽  
Current Knowledge ◽  
Life Quality ◽  
Sub Saharan Africa ◽  
Ross River Virus ◽  
Pacific Island ◽  
The Pacific ◽  
Sub Saharan ◽  
Mayaro Virus

Arthritogenic alphaviruses are responsible for a dengue-like syndrome associated with severe debilitating polyarthralgia that can persist for months or years and impact life quality. Chikungunya virus is the most well-known member of this family since it was responsible for two worldwide epidemics with millions of cases in the last 15 years. However, other arthritogenic alphaviruses that are as of yet restrained to specific territories are the cause of neglected tropical diseases: O’nyong’nyong virus in Sub-Saharan Africa, Mayaro virus in Latin America, and Ross River virus in Australia and the Pacific island countries and territories. This review evaluates their emerging potential in light of the current knowledge for each of them and in comparison to chikungunya virus.

scholarly journals Development of Common Bean (Phaseolus Vulgaris L.) Production Under Low Soil Phosphorus and Drought in Sub-Saharan Africa: A Review

2014 ◽  
Vol 7 (5) ◽  
Author(s):  
Margaret Namugwanya ◽  
John Stephen Tenywa ◽  
Erasmus Otabbong ◽  
Drake N. Mubiru ◽  
Twaha Ali Masamba
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Soil Phosphorus ◽  
Sub Saharan Africa ◽  
Phaseolus Vulgaris L ◽  
Sub Saharan

scholarly journals Phylogeny of African complete genomes reveals a West African genotype A subtype of hepatitis B virus and relatedness between Somali and Asian A1 sequences

2005 ◽  
Vol 86 (8) ◽  
pp. 2163-2167 ◽  
Author(s):  
Charles Hannoun ◽  
Ann Söderström ◽  
Gunnar Norkrans ◽  
Magnus Lindh
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
West African ◽  
Sub Saharan Africa ◽  
Start Codon ◽  
Southern Asia ◽  
B Virus ◽  
Complete Genomes ◽  
Sub Saharan ◽  
Genotype A

Hepatitis B virus (HBV) is a major cause worldwide of liver disease, including hepatocellular carcinoma. There are eight known genotypes (A–H), of which genotype A has been divided into two subtypes: A2, prevalent in Europe, and A1, which is prevalent in sub-Saharan Africa, but also occurs in southern Asia. In this study, which includes 14 new complete genomes of non-European genotype A HBV, it was found that West African strains seem to constitute a new subgroup, A3. The high degree of genetic diversity within Africa indicates that genotype A originates from Africa. Based on a 2 % genetic distance between Asian and Somali sequences, it seems that the A1 subtype has spread from East Africa to southern Asia during the last 1000–2000 years. Moreover, it is proposed here that the A2 subtype originates from southern Africa and was imported to Europe around 500 years ago or later. The finding of T-1809/1812 close to the precore start codon and T-1862 and A-1888 in the precore region in HBV e antigen-positive children with signs of a mimimal immune response indicates that these substitutions are stable variants, rather than mutations emerging during infection in individual carriers.

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