scholarly journals Genomic Diversity and Phylogenetic Analysis of SARS-CoV-2 Circulating in Africa and Other Continents: Implications for Diagnosis, Transmission, and Prevention

2020 ◽  
Vol 4 (3) ◽  
Author(s):  
Idowu A. Taiwo
Keyword(s):  
Genome Sequence ◽  
Genetic Relatedness ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Phase 1 ◽  
Threat Assessment ◽  
Population Based ◽  
Genomic Diversity ◽  
Sequence Length ◽  
Phase 2

Background: COVID-19 pandemic caused by SARS-CoV-2 remains a global health threat. Assessment of the genetic relatedness of the genome sequence is a prerequisite to understanding the dynamics, which is important to improve diagnosis and preventive measures. This study determined genomic diversity and SNP characteristic of genomes of SARS-CoV-2 from Africa and the rest of the world. The study involved molecular and phylogenetic analyses to understand the phylogeny and transmission dynamics of the virus. Methods: The SARS-CoV-2 genome sequence data were mined and retrieved from major databases for one year in two phases: Phase 1; December 2019 to May 2020 and Phase 2; June 2020 to December 2020. A maximum of the four sequences that fulfilled the following predetermined criteria from each country were randomly selected for inclusion in the study: (i) sequence length >29,700 nt, (ii) number of Ns in the sequence not >5%, (iii) inclusion of Poly-A tail in the sequence record to ensure completeness. Results: The similarity of SARS-Cov-2 genomes within and between countries was generally high with an average of 99.9%. Thus, SARS-CoV-2 vary between countries and continents by 0.1% as a result of SNPs in its genome. Phylogenetic data revealed multiple origin of SARS-CoV-2 in Africa and also suggested that the virus spreads by ‘founder’s effect’; whereby few viruses newly introduced into a population multiply rapidly and accumulate mutations as they spread quickly by community transfer to create population-based identity. Tree of continental consensus sequences retrieved in Phase 1 suggested that SARS-CoV-2 virus is of two major clusters: African cluster consisting of Africa, Europe, and North America and Asian cluster made up of Asia, South America, and Oceania. However, this clustering pattern vanished in phase 2. Thus, upholding the view that SARS-CoV-2 is constantly evolving. Conclusion: This dynamism and genetic diversity of SARS-CoV-2 have important implications in diagnosis, transmission, and prevention strategy.

scholarly journals Population-based virucidal phthalocyanine gargle/rinse protocol to reduce the risk of coronavirus disease-2019: a community trial

2021 ◽  
Author(s):  
Verônica Caroline Brito Reia ◽  
Roosevelt da Silva Bastos ◽  
Fabiano Vieira Vilhena ◽  
Heitor Marques Honório ◽  
Lucas Marques da Costa Alves ◽  
...  
Keyword(s):  
Relative Risk ◽  
Disease Risk ◽  
Phase 1 ◽  
Population Level ◽  
Population Based ◽  
Phase 2 ◽  
Control Community ◽  
And Control ◽  
Official Information ◽  
Community Trial

Abstract Purpose: In this community trial, the objective was to evaluate the incidence of coronavirus disease-2019 (COVID-19) cases in two similar communities in three distinct phases: phase 1 (before the intervention), 2 (during the intervention), and 3 (after the intervention).Methods: The test community received the oral antiseptic intervention (experimental), while the control community did not. The official information agency provided the number of confirmed COVID-19 cases. Data were analyzed according to the three phases per epidemiological week (epi) using the R Core Team (2021) program. The relative risk and 95% confidence intervals between the cumulative incidence values of the test and control communities were calculated for each period. In the test community, a total of 995 residents, over 10 years of age, received two bottles containing 600 ml of mouthwash with antiviral phthalocyanine derivative (APD). The participants were asked to gargle/rinse with of 5 mL of the mouthwash with ADP 3 to 5 times a day, for 1 min, until the end of the bottles. Results: In phases 1 and 3, disease risk between the two communities did not differ significantly (p> 0.05), while in phase 2, disease risk was 54% lower in the test community than in the control community. Conclusion: The use of the APD mouthwash protocol seems to reduce the COVID-19 incidence at the population level, and further studies are needed to confirm its protective effect in different contexts.

scholarly journals A comparative analysis of family-based and population-based association tests using whole genome sequence data

2014 ◽  
Vol 8 (Suppl 1) ◽  
pp. S33 ◽  
Author(s):  
Jin J Zhou ◽  
Wai-Ki Yip ◽  
Michael H Cho ◽  
Dandi Qiao ◽  
Merry-Lynn N McDonald ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Genome Sequence ◽  
Sequence Data ◽  
Population Based ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Association Tests ◽  
Genome Sequence Data ◽  
Family Based

scholarly journals Genome sequence of a waterfowl aviadenovirus, goose adenovirus 4

2012 ◽  
Vol 93 (11) ◽  
pp. 2457-2465 ◽  
Author(s):  
Győző L. Kaján ◽  
Andrew J. Davison ◽  
Vilmos Palya ◽  
Balázs Harrach ◽  
Mária Benkő
Keyword(s):  
Genome Sequence ◽  
Central Region ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Genome Sequences ◽  
Limited Sequence

We present, to our knowledge, the first complete genome sequence of a waterfowl aviadenovirus, goose adenovirus (GoAdV) strain P29, and an analysis of its genetic content in comparison with five published aviadenovirus genome sequences. Of the 35 genes predicted to encode functional proteins, the central region of the genome contains 19 (IVa2 to fiber-2) that were inherited from the ancestor of all known adenoviruses. Of the remaining genes, nine have orthologues only in aviadenoviruses and seven lack orthologues in any adenovirus. We also obtained limited sequence data for a pathogenic GoAdV strain D1036/08. Phylogenetic analyses placed the two GoAdV strains monophyletically in the genus Aviadenovirus. We propose designating strains P29 and D1036/08 as GoAdV-4 and GoAdV-5, respectively.

scholarly journals Blueprint for Phasing and Assembling the Genomes of Heterozygous Polyploids: Application to the Octoploid Genome of Strawberry

2021 ◽  
Author(s):  
Michael A Hardigan ◽  
Mitchell J Feldmann ◽  
Dominique DA Pincot ◽  
Randi A Famula ◽  
Michaela V Vachev ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phase 1 ◽  
Diploid Species ◽  
Significant Risk ◽  
Allelic Diversity ◽  
Recombination Breakpoint ◽  
Genomic Research ◽  
Phase 2 ◽  
Direct Assembly ◽  
Gold Standard Reference

The challenge of allelic diversity for assembling haplotypes is exemplified in polyploid genomes containing homoeologous chromosomes of identical ancestry, and significant homologous variation within their ancestral subgenomes. Cultivated strawberry (Fragaria x ananassa) and its wild progenitors are outbred octoploids (2n = 8x = 56) in which up to eight homologous and homoeologous alleles are preserved. This introduces significant risk of haplotype collapse, switching, and chimeric fusions during assembly. Using third generation HiFi sequences from PacBio, we assembled the genome of the day-neutral octoploid F. x ananassa hybrid 'Royal Royce' from the University of California. Our goal was to produce subgenome- and haplotype-resolved assemblies of all 56 chromosomes, accurately reconstructing the parental haploid chromosome complements. Previous work has demonstrated that partitioning sequences by parental phase supports direct assembly of haplotypes in heterozygous diploid species. We leveraged the accuracy of HiFi sequence data with pedigree-informed sequencing to partition long read sequences by phase, and reduce the downstream risk of subgenomic chimeras during assembly. We were able to utilize an octoploid strawberry recombination breakpoint map containing 3.6 M variants to identify and break chimeric junctions, and perform scaffolding of the phase-1 and phase-2 octoploid assemblies. The N50 contiguity of the phase-1 and phase-2 assemblies prior to scaffolding and gap-filling was 11 Mb. The final haploid assembly represented seven of 28 chromosomes in a single contiguous sequence, and averaged fewer than three gaps per pseudomolecule. Additionally, we re-annotated the octoploid genome to produce a custom F. x ananassa repeat library and improved set of gene models based on IsoSeq transcript data and an expansive RNA-seq expression atlas. Here we present 'FaRR1', a gold-standard reference genome of F. x ananassa cultivar 'Royal Royce' to assist future genomic research and molecular breeding of allo-octoploid strawberry.

scholarly journals Recombination Events Shape the Genomic Evolution of Infectious Bronchitis Virus in Europe

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 535
Author(s):  
Krisztina Bali ◽  
Ádám Bálint ◽  
Attila Farsang ◽  
Szilvia Marton ◽  
Borbála Nagy ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Infectious Bronchitis Virus ◽  
Hot Spots ◽  
Sequence Data ◽  
Genomic Diversity ◽  
Data Set ◽  
Genome Sequence Data ◽  
Infectious Bronchitis ◽  
Recombination Hot Spots ◽  
Multiple Recombination

Infectious bronchitis of chicken is a high morbidity and mortality viral disease affecting the poultry industry worldwide; therefore, a better understanding of this pathogen is of utmost importance. The primary aim of this study was to obtain a deeper insight into the genomic diversity of field infectious bronchitis virus (IBV) strains using phylogenetic and recombination analysis. We sequenced the genome of 20 randomly selected strains from seven European countries. After sequencing, we created a genome sequence data set that contained 36 European origin field isolates and 33 vaccine strains. When analyzing these 69 IBV genome sequences, we identified 215 recombination events highlighting that some strains had multiple recombination breaking points. Recombination hot spots were identified mostly in the regions coding for non-structural proteins, and multiple recombination hot spots were identified in the nsp2, nsp3, nsp8, and nsp12 coding regions. Recombination occurred among different IBV genotypes and involved both field and vaccine IBV strains. Ninety percent of field strains and nearly half of vaccine strains showed evidence of recombination. Despite the low number and the scattered geographical and temporal origin of whole-genome sequence data collected from European Gammacoronaviruses, this study underlines the importance of recombination as a major evolutionary mechanism of IBVs.

scholarly journals Canadian Collaborative Project on Genetic Susceptibility to MS, Phase 2: Rationale and Method

1998 ◽  
Vol 25 (3) ◽  
pp. 216-221 ◽  
Author(s):  
A.D. Sadovnick ◽  
N.J. Risch ◽  
G.C. Ebers ◽  
Keyword(s):  
Genetic Susceptibility ◽  
Familial Aggregation ◽  
Phase 1 ◽  
Molecular Genetic ◽  
Genetic Research ◽  
Population Based ◽  
Phase 2 ◽  
Genetic Studies ◽  
Collaborative Project ◽  
Index Cases

ABSTRACT:Background:Results from the Canadian Collaborative Project on Genetic Susceptibility to Multiple Sclerosis (MS)-Phase 1 (CCPGSMS-Phase 1) together with other family data published since 1982 have led to the following conclusions about the etiology of MS: (i) genetic and non-genetic (environmental) factors are involved in the etiology of MS on a population basis; (ii) the familial aggregation of MS is genetic; (iii) maternal factors do not influence the risk for siblings to develop MS; and (iv) MS appears to be oligogenic. The present paper describes the rationale and methodology for the CCPGSMS-Phase 2.Methods:The CCPGSMS-Phase 2 is a nation-wide collaborative effort involving all the 15 Canadian MS clinics. A series of structured questionnaires is administered to MS index cases, spouse controls and mothers of index cases and spouse controls (if available) by trained interviewers. Blood samples are taken for molecular genetic studies. This national effort is coordinated by the MS Clinics in Vancouver and London.Results:The CCPGSMS-Phase 2 is in progress so specific results are not available. The study is designed to (i) increase the database for genetic epidemiological/molecular genetic research and (ii) gather population-based data to further our understanding of the non-genetic factors in the etiology of MS.Conclusions:It is anticipated that the results from this study will impact on the eventual prevention, cure and treatment of MS.

Genetic variation of the greenhouse whitefly, Trialeurodes vaporariorum (Hemiptera: Aleyrodidae), among populations from Serbia and neighbouring countries, as inferred from COI sequence variability

2014 ◽  
Vol 104 (3) ◽  
pp. 357-366 ◽  
Author(s):  
M. Prijović ◽  
M. Škaljac ◽  
T. Drobnjaković ◽  
K. Žanić ◽  
P. Perić ◽  
...  
Keyword(s):  
Genetic Relatedness ◽  
Sequence Data ◽  
Spatial Genetic Structure ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Trialeurodes Vaporariorum ◽  
Plant Viruses ◽  
Sequence Variability ◽  
Greenhouse Whitefly ◽  
The Usa

AbstractThe greenhouse whitefly Trialeurodes vaporariorum Westwood, 1856 (Hemiptera: Aleyrodidae) is an invasive and highly polyphagous phloem-feeding pest of vegetables and ornamentals. Trialeurodes vaporariorum causes serious damage due to direct feeding and transmits several important plant viruses. Excessive use of insecticides has resulted in significantly reduced levels of susceptibility of various T. vaporariorum populations. To determine the genetic variability within and among populations of T. vaporariorum from Serbia and to explore their genetic relatedness with other T. vaporariorum populations, we analysed the mitochondrial cytochrome c oxidase I (COI) sequences of 16 populations from Serbia and six neighbouring countries: Montenegro (three populations), Macedonia (one population) and Croatia (two populations), for a total of 198 analysed specimens. A low overall level of sequence divergence and only five variable nucleotides and six haplotypes were found. The most frequent haplotype, H1, was identified in all Serbian populations and in all specimens from distant localities in Croatia and Macedonia. The COI sequence data that was retrieved from GenBank and the data from our study indicated that H1 is the most globally widespread T. vaporariorum haplotype. A lack of spatial genetic structure among the studied T. vaporariorum populations, as well as two demographic tests that we performed (Tajima's D value and Fu's Fs statistics), indicate a recent colonisation event and population growth. Phylogenetic analyses of the COI haplotypes in this study and other T. vaporariorum haplotypes that were retrieved from GenBank were performed using Bayesian inference and median-joining (MJ) network analysis. Two major haplogroups with only a single unique nucleotide difference were found: haplogroup 1 (containing the five Serbian haplotypes and those previously identified in India, China, the Netherlands, the United Kingdom, Morocco, Reunion and the USA) and haplogroup 3 (containing the single Serbian haplotype H3 and haplotypes from Costa Rica, the USA and Spanish Canary Islands). Collectively, our data indicate a rather limited value of COI as a genetic marker for discrimination between different T. vaporariorum populations in the investigated area. Possible explanations for the observed lack of COI sequence variability, such as specific genetics of biological invasion and/or the influence of bacterial symbionts that manipulate insect reproduction, are discussed.

scholarly journals Serial population-based sero-surveys for COVID-19 in low and high transmission neighborhoods of urban Pakistan

2020 ◽  
Author(s):  
Muhammad Imran Nisar ◽  
Nadia Ansari ◽  
Farah Khalid ◽  
Mashal Amin ◽  
Hamna Shahbaz ◽  
...  
Keyword(s):  
Phase 1 ◽  
Parametric Bootstrap ◽  
Population Based ◽  
Bayesian Regression ◽  
Phase 2 ◽  
Phase 3 ◽  
Cross Sectional ◽  
Conditional Risk ◽  
High Transmission ◽  
Later Phase

AbstractObjectiveTo determine population-based estimates of COVID-19 in a densely populated urban community of Karachi, Pakistan.MethodsThree cross-sectional surveys were conducted in April, June and August in low- and high-transmission neighborhoods of Karachi. Participants were randomly selected to provide blood for Elecsys® immunoassay for detection of anti-SARS-CoV-2 antibodies. Bayesian regression model was used to estimate seroprevalence after adjusting for the demographic characteristics of each district. Conditional Risk of Infection (CRI) with 95% confidence interval was calculated using a non-parametric bootstrap of households. Infection fatality rates (IFR) were estimated.ResultsWe enrolled 3005 participants from 623 households. In Phase 2, the adjusted seroprevalence was estimated as 8.7% (95% CI 5.1-13.1) and 15.1% (95% CI 9.4 -21.7) in low and high transmission areas respectively, compared to 0.2% (95% CI 0-0.7) and 0.4% (95% CI 0 - 1.3) in Phase 1. In Phase 3, it was 12.8% (95% CI 8.3 – 17.7) and 21.5% (95% CI 15.6-28) in low and high transmission areas, respectively. CRI was 0.31 (95% CI 0.16-0.47) and 0.41(95% CI 0.28-0.52) in low and high transmission neighborhoods respectively in Phase 2. Similar trends were observed in Phase 3. Only 5.4% of participants who tested positive for COVID-19 were symptomatic. IFR was 1.66% in phase 1, 0.37% in Phase 2 and 0.26% in Phase 3.ConclusionInitial rapid increase in seroprevalence was followed by a plateau in the later phase of the pandemic in Karachi. Continuing rounds of seroprevalence studies have the potential to fully characterize the pandemic in this geography.

Rationalization and internalization

2001 ◽  
Vol 60 (4) ◽  
pp. 215-230 ◽  
Author(s):  
Jean-Léon Beauvois
Keyword(s):  
Phase 1 ◽  
Facilitatory Effect ◽  
Phase 2 ◽  
Causal Explanations ◽  
Reduction Effect ◽  
Dissonance Reduction

After having been told they were free to accept or refuse, pupils aged 6–7 and 10–11 (tested individually) were led to agree to taste a soup that looked disgusting (phase 1: initial counter-motivational obligation). Before tasting the soup, they had to state what they thought about it. A week later, they were asked whether they wanted to try out some new needles that had supposedly been invented to make vaccinations less painful. Agreement or refusal to try was noted, along with the size of the needle chosen in case of agreement (phase 2: act generalization). The main findings included (1) a strong dissonance reduction effect in phase 1, especially for the younger children (rationalization), (2) a generalization effect in phase 2 (foot-in-the-door effect), and (3) a facilitatory effect on generalization of internal causal explanations about the initial agreement. The results are discussed in relation to the distinction between rationalization and internalization.

Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

2019 ◽  
Vol 44 (4) ◽  
pp. 930-942
Author(s):  
Geraldine A. Allen ◽  
Luc Brouillet ◽  
John C. Semple ◽  
Heidi J. Guest ◽  
Robert Underhill
Keyword(s):  
North American ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Morphological Evidence ◽  
South American ◽  
New Combinations ◽  
The North ◽  
Hybridization Event ◽  
Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

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