scholarly journals Infection with different strains of SARS-COV-2 in patients with COVID-19

2020 ◽  
Vol 72 (4) ◽  
pp. 575-585 ◽  
Author(s):  
Hayder Hashim ◽  
Mudher Mohammed ◽  
Mazin Mousa ◽  
Hadeer Abdulameer ◽  
Alaa Alhassnawi ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
High Frequency ◽  
Biological Diversity ◽  
Viral Infections ◽  
Phylogenetic Analyses ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Single Strain ◽  
Different Strains ◽  
Multiple Strains

The biological diversity of SARS-CoV-2 was assessed by investigating the genetic variations of the spike glycoprotein of patients with COVID-19 in Iraq. Sequencing identified fifteen novel nucleic acid variations with a variety of distributions within the investigated samples. The electropherograms of all identified variations showed obvious co-infections with two different viral strains per sample. Most samples exhibited three nonsense single nucleotide polymorphism (SNPs), p.301Cdel, p.380Ydel and p.436del, which yielded three truncated spike glycoproteins, respectively. Network and phylogenetic analyses indicated that all viral infections were derived from multiple viral origins. Results inferred from the specific clade-based tree showed that some viral strains were derived from European G-clade sequences. Our data demonstrated the absence of single-strain infection among all investigated samples in the studied area, which entails a higher risk of SARS-CoV-2 in this country. The identified high frequency of truncated spike proteins suggests that defective SARS-CoV-2 depend on helper strains possessing intact spikes during infection. Alternatively, another putative ACE2-independent route of viral infection is suggested. To the best of our knowledge, this is the first report to describe co-infection with multiple strains of SARS-CoV-2 in patients with COVID-19.

scholarly journals Unexpected Co-infection with Different Strains of SARS-CoV-2 in Patients with COVID-19

2020 ◽  
Author(s):  
Hayder O. Hashim ◽  
Mudher K. Mohammed ◽  
Mazin J. Mousa ◽  
Hadeer H. Abdulameer ◽  
Alaa T.S. Alhassnawi ◽  
...  
Keyword(s):  
Biological Diversity ◽  
Viral Infections ◽  
Transmission Rate ◽  
Phylogenetic Analyses ◽  
Coding Region ◽  
Spike Glycoprotein ◽  
Single Strain ◽  
Different Strains ◽  
Multiple Strains

There is a rising global concern for the ongoing outbreak of SARS-CoV-2 due to its high transmission rate and unavailability of treatment. Through the binding of its spike glycoprotein with angiotensin type 2 (ACE2), SARS-CoV-2 can efficiently get in the cells of patients and start its pandemic cycle. Herein, the biological diversity of SARS-CoV-2 infection was assessed in Babylon province of Iraq by investigating the possible genetic variations of the spike glycoprotein. A specific coding region of 795 bp within the viral spike (S) gene was amplified from 19 patients who suffered from obvious symptoms of SARS-CoV-2 infection. Sequencing results identified fifteen novel nucleic acid variations with a variety of distributions within the investigated samples. The electropherograms of all the identified variations showed obvious co-infections with at least two different viral strains per sample. Within these co-infections, the majority of samples exhibited three nonsense single nucleotide polymorphism (SNP)s, p.301Cdel, p.380Ydel, and p.436del, which yielded three truncated SARS-CoV-2 spike glycoproteins of 301, 380, and 436 amino acids length, respectively. The network and phylogenetic analyses indicated that for all viral infections were derived from multi-ancestral origins. Results inferred from the specific clade-based tree entailed that some viral strains were derived from European G-clade sequences. In conclusion, our data demonstrated the absence of any single strain infection among all investigated viral samples in the studied area, which may entail a higher risk of SARS-CoV-2 in this country. Through the identified high frequency of truncated spike proteins, we suggest that defective SARS-CoV-2 may depend on helper strains having intact spikes in its infection. Alternatively, another putative ACE2-independent route of viral infection way also suggested. To the best of our knowledge, this is the first report to describe the co-infection of multiple strains of SARS-CoV-2 in patients with COVID-19.

scholarly journals Synthetic and Evolutionary Construction of a Chlorate-Reducing Shewanella oneidensis MR-1

mBio ◽  
2015 ◽  
Vol 6 (3) ◽  
Author(s):  
Iain C. Clark ◽  
Ryan A. Melnyk ◽  
Matthew D. Youngblut ◽  
Hans K. Carlson ◽  
Anthony T. Iavarone ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Copy Number ◽  
Shewanella Oneidensis ◽  
Respiratory Metabolism ◽  
Chromosome 11 ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Single Strain ◽  
Content Type ◽  
Essential Components

ABSTRACTDespite evidence for the prevalence of horizontal gene transfer of respiratory genes, little is known about how pathways functionally integrate within new hosts. One example of a mobile respiratory metabolism is bacterial chlorate reduction, which is frequently encoded on composite transposons. This implies that the essential components of the metabolism are encoded on these mobile elements. To test this, we heterologously expressed genes for chlorate reduction fromShewanella algaeACDC in the non-chlorate-reducingShewanella oneidensisMR-1. The construct that ultimately endowed robust growth on chlorate includedcld, a cytochromecgene,clrABDC, and two genes of unknown function. Although strain MR-1 was unable to grow on chlorate after initial insertion of these genes into the chromosome, 11 derived strains capable of chlorate respiration were obtained through adaptive evolution. Genome resequencing indicated that all of the evolved chlorate-reducing strains replicated a large genomic region containing chlorate reduction genes. Contraction in copy number and loss of the ability to reduce chlorate were also observed, indicating that this phenomenon was extremely dynamic. Although most strains contained more than six copies of the replicated region, a single strain with less duplication also grew rapidly. This strain contained three additional mutations that we hypothesized compensated for the low copy number. We remade the mutations combinatorially in the unevolved strain and determined that a single nucleotide polymorphism (SNP) upstream ofcldenabled growth on chlorate and was epistatic to a second base pair change in the NarP binding sequence betweennarQPandnrfAthat enhanced growth.IMPORTANCEThe ability of chlorate reduction composite transposons to form functional metabolisms after transfer to a new host is an important part of their propagation. To study this phenomenon, we engineeredShewanella oneidensisMR-1 into a chlorate reducer. We defined a set of genes sufficient to endow growth on chlorate from a plasmid, but found that chromosomal insertion of these genes was nonfunctional. Evolution of this inoperative strain into a chlorate reducer showed that tandem duplication was a dominant mechanism of activation. While copy number changes are a relatively rapid way of increasing gene dosage, replicating almost 1 megabase of extra DNA is costly. Mutations that alleviate the need for high copy number are expected to arise and eventually predominate, and we identified a single nucleotide polymorphism (SNP) that relieved the copy number requirement. This study uses both rational and evolutionary approaches to gain insight into the evolution of a fascinating respiratory metabolism.

scholarly journals High frequency of the PNPLA3 rs738409 [G] single-nucleotide polymorphism in Hmong individuals as a potential basis for a predisposition to chronic liver disease

Cancer ◽  
2018 ◽  
Vol 124 ◽  
pp. 1583-1589 ◽  
Author(s):  
Clifford G. Tepper ◽  
Julie H. T. Dang ◽  
Susan L. Stewart ◽  
Dao M. Fang ◽  
Kimberly A. Wong ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Liver Disease ◽  
Chronic Liver Disease ◽  
High Frequency ◽  
Chronic Liver ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Potential Basis

scholarly journals Frequency of Polyploids of Solanum tuberosum Dihaploids in 2X × 2X Crosses

2021 ◽  
pp. 76-80
Author(s):  
Susan A. Otieno ◽  
Joseph Coombs ◽  
David S. Douches
Keyword(s):  
Single Nucleotide Polymorphism ◽  
High Frequency ◽  
2N Pollen ◽  
Sexual Polyploidization ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
2N Eggs ◽  
Bilateral Sexual Polyploidization ◽  
Tetraploid Progeny

When breeding diploid potatoes, tetraploid progeny can result from the union of 2n eggs and 2n pollen in 2x-2x crosses. Thirty-three crosses were made to examine tetraploid progeny frequency in 2x-2x crosses. All crosses were between S. tuberosum dihaploids and diploid self-compatible donors, M6 and DRH S6-10-4P17. Using chloroplast counting for ploidy determination, the frequency of tetraploid progeny was as high as 45% in one of the 33 crosses. Based upon single nucleotide polymorphism (SNP) genotyping, the tetraploid progeny were attributed to bilateral sexual polyploidization (BSP), which is caused by the union of 2n egg and 2n pollen. Dihaploids were identified that produce lower frequencies of 2n eggs. The results of this study suggest that S. tuberosum dihaploids with a high frequency of 2n eggs should be avoided in 2x - 2x crosses for diploid breeding programs.

UTILIZATION OF DNA MARKERS FOR EVALUATING AMYLOSE CONTENT OF GRAIN IN RICE

2013 ◽  
Vol 83 (5) ◽  
Author(s):  
Dương Thanh Thủy ◽  
Taiichiro Ookawa
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Amylose Content ◽  
Waxy Gene ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Branching Enzymes ◽  
Wx Gene ◽  
High Amylose ◽  
Suitable Marker ◽  
Granule Bound Starch Synthase

The sensory and functional properties of rice are predominantly associated with its amylose content. Granule-bound starch synthase (GBSS) encoded by the Waxy (Wx) gene determines the synthesis of amylose, while starch branching enzymes encoded by Sbe genes are involved in the formation of amylopectin. Some studies have demonstrated that Wx gene is the major controller of amylose content but there are one or more modifying genes affecting the amylose content. Three markers,  microsatellite, Single – nucleotide – polymorphism (G/T SNP) in Wx gene and Single – nucleotide – polymorphism (T/C SNP) in Sbe1 gene, were tested for their association with amylose content using sixty-nine  rice accessions from twenty countries. Of the three markers, two markers in Wx gene are significantly associated with amylose content. The combination of two markers in Wx gene (haplotypes) explained 83.8% of the variation in amylose content and discriminated the three market classes of glutinous, low, intermediate and high amylose content of rice from each other. And T/C SNP in Sbe1 locus was not a suitable marker for amylose content. Keywords: marker, amylose content, Waxy gene.

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