scholarly journals Genomic diversity of SARS-CoV-2 in Malaysia

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12449
Author(s):  
Noorliza Mohamad Noordin ◽  
Joon Liang Tan ◽  
Chee Kheong Chong ◽  
Yu Kie Chem ◽  
Norazimah Tajudin ◽  
...  
Keyword(s):  
Minimum Spanning Tree ◽  
Genomic Diversity ◽  
Epidemiological Surveillance ◽  
First Year ◽  
Evolutionary Trend ◽  
Genetic Changes ◽  
Association Analyses ◽  
Viral Genomes ◽  
National Public Health ◽  
Genetic Clustering

Background More than a year after its first appearance in December 2019, the COVID-19 pandemic is still on a rampage in many parts of the world. Although several vaccines have been approved for emergency use, the emergence and rapid spread of new SARS-CoV-2 variants have sparked fears of vaccine failure due to immune evasion. Massive viral genome sequencing has been recommended to track the genetic changes that could lead to adverse consequences. Methods We sequenced SARS-CoV-2 respiratory isolates from the National Public Health Laboratory, Malaysia and examined them together with viral genomes deposited in GISAID by other Malaysian researchers, to understand the evolutionary trend of the virus circulating in the country. We studied the distribution of virus lineages and site-wise mutations, analysed genetic clustering with the goeBURST full Minimum Spanning Tree algorithm, examined the trend of viral nucleotide diversity over time and performed nucleotide substitution association analyses. Results We identified 22 sub-lineages, 13 clonal complexes, 178 sequence types and seven sites of linkage disequilibrium in 277 SARS-CoV-2 genomes sequenced between January and December 2020. B.1.524 was the largest lineage group. The number of mutations per genome ranged from 0 to 19. The mean genomic diversity value over 12 months was 3.26 × 10−4. Of 359 mutations detected, 60.5% of which were non-synonymous, the most frequent were in the ORF1ab (P4715L), S (D614G and A701V) and N (S194L) genes. Conclusion The SARS-CoV-2 virus accumulated an abundance of mutations in the first year of the COVID-19 pandemic in Malaysia. Its overall genetic diversity, however, is relatively low compared to other Asian countries with larger populations. Continuous genomic and epidemiological surveillance will help to clarify the evolutionary processes determining viral diversity and impacting on human health.

scholarly journals Convergent evolution in Arabidopsis halleri and Arabidopsis arenosa on calamine metalliferous soils

2018 ◽  
Author(s):  
Veronica Preite ◽  
Christian Sailer ◽  
Lara Syllwasschy ◽  
Sian Bray ◽  
Ute Krämer ◽  
...  
Keyword(s):  
Convergent Evolution ◽  
Arabidopsis Halleri ◽  
Individual Genome ◽  
Genetic Changes ◽  
Association Analyses ◽  
Systematic Testing ◽  
Related Plant ◽  
Arabidopsis Arenosa ◽  
Species Specific ◽  
Degree Of Convergence

AbstractIt is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, Arabidopsis halleri and Arabidopsis arenosa, which co-occur at two calamine metalliferous sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from 8 populations on metalliferous and non-metalliferous soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical SNPs in several A. halleri genes at two independently colonized metalliferous sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine metalliferous soils involves convergent evolution, which will likely be more pervasive across sites purposely chosen for maximal similarity in soil composition.

scholarly journals A67 Bloodstream infections by carbapenem-resistant Klebsiella pneumoniae subsp. pneumoniae: Bayesian phylogenetic analysis of whole genomes

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
Eleonora Cella ◽  
Davide Leoni ◽  
Walter Mirandola ◽  
Carla Fontana ◽  
Loredana Sarmati ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Klebsiella Pneumoniae ◽  
Infection Control ◽  
Minimum Spanning Tree ◽  
Hospital Setting ◽  
Bloodstream Infections ◽  
Multidrug Resistant ◽  
Epidemiological Surveillance ◽  
Health Concern ◽  
Hospital Infection Control

Abstract Bloodstream infection (BSI) caused by carbapenemase-producing Enterobacteriaceae (CPE) is a major public health concern, particularly in the hospital setting. The rapid detection of resistance patterns is of paramount importance for establishing the proper antibiotic regime. In addition, in countries where CPE are endemic, it is also important to evaluate genetic relationship among the isolates in order to trace pathogen circulation and to improve the infection control programs. This study is an application of a rapid blood culture (BC) workflow consisting of fast reporting of Gram stain results, rapid pathogen identification (using MALDI TOF technology), and a molecular assay for the detection of the major genes conferring resistance, all of them performed directly from positive BCs. The application of phylogenetic and phylodynamic analyses to bacterial whole-genome sequencing (WGS) data have become essential in the epidemiological surveillance of multidrug-resistant nosocomial pathogens. We analyzed 40 strains of Klebsiella pneumoniae subsp. pneumoniae (KP) carrying blaKPC (KP-KPC), randomly selected among 147 CPE identified from BCs collected from consecutive patients from 2013 to 2016. The number of BSIs-related CPE were 23, 31, 43, and 50 in 2013, 2014, 2015, and 2016, respectively. Among 147 CPE isolates, 143 were KP and four were Escherichia coli (EC). The gene blaKPC was detected in 117 strains of KP and in four strains of EC. Other carbapenemase genes, such as blaVIM and blaOXA-48, were detected in four and nine different isolates of KP, respectively. Moreover, 13 KP strains carried two resistance genes: twelve vehicled blaKPC plus blaVIM and one blaKPC plus blaOXA-48. Phylogenetic analysis of bacterial WGS data was used to investigate the evolution and spatial dispersion of KP in support of hospital infection control. The maximum likelihood tree showed two main clades statistically supported, with statistical support for several subclusters within as well. The minimum spanning tree showed mixing between sequences from different years and wards with only few specific groups. Bayesian analyses are ongoing, as the aid of Bayesian genomic epidemiology in combination with active microbial surveillance is highly informative regarding the development of effective infection prevention in healthcare settings or constant strain reintroduction.

scholarly journals Unprecedented increase of West Nile virus neuroinvasive disease, Spain, summer 2020

2021 ◽  
Vol 26 (19) ◽  
Author(s):  
Lucía García San Miguel Rodríguez-Alarcón ◽  
Beatriz Fernández-Martínez ◽  
María José Sierra Moros ◽  
Ana Vázquez ◽  
Paula Julián Pachés ◽  
...  
Keyword(s):  
Public Health ◽  
West Nile Virus ◽  
Vector Control ◽  
Epidemiological Surveillance ◽  
West Nile ◽  
Surveillance Network ◽  
Vector Borne Diseases ◽  
Health Measures ◽  
Neuroinvasive Disease ◽  
National Public Health

Cases of West Nile neuroinvasive disease (WNND) in Spain increased in summer 2020. Here we report on this increase and the local, regional and national public health measures taken in response. We analysed data from regional surveillance networks and the National Epidemiological Surveillance Network, both for human and animal West Nile virus (WNV) infection. During the 2020 season, a total of 77 human cases of WNV infection (median age 65 years; 60% males) were detected in the south-west of Spain; 72 (94%) of these cases developed WNND, presenting as meningoencephalitis, seven of which were fatal. In the previous two decades, only six human cases of WNND were detected in Spain. Reduced activities for vector control this season, together with other factors, might have contributed to the massive increase. Public health measures including vector control, campaigns to raise awareness among physicians and the general population, and interventions to ensure the safety of donations of blood products, organs, cells and tissues were effective to reduce transmission. Going forward, maintenance of vector control activities and an update of the vector-borne diseases response plan in Spain is needed.

scholarly journals Association study of long-term kidney transplant rejection using whole-exome sequencing

2018 ◽  
Author(s):  
Louis Gioia ◽  
Sunil Kurian ◽  
Tony S. Mondala ◽  
Laia Bassaganyas ◽  
Pui-Yan Kwok ◽  
...  
Keyword(s):  
Interstitial Fibrosis ◽  
Transplant Rejection ◽  
Study Data ◽  
First Year ◽  
Post Transplantation ◽  
Tubular Atrophy ◽  
Association Analyses ◽  
Analysis Workflow ◽  
Meta Analyses

AbstractLong-term renal allograft rejection is the most common outcome in kidney transplantation. Continuing the crusade to extend allograft function after the first year post-transplantation, we attempted to associate genetic factors that might contribute to long-term allograft outcomes by sequencing the exomes of patients diagnosed with chronic allograft nephropathy/interstitial fibrosis and tubular atrophy. A variety of association analyses were employed, but these analyses failed to identify statistically significant associations. The study was underpowered to detect the association of rare genomic variants with small effect sizes. However, it confirmed previous reports of the absence of large effects from common variants. We have made both the study data and analysis workflow available for public use, and we hope that these resources will help to power future meta-analyses that may detect smaller effects.

scholarly journals Concerted variation in melanogenesis genes underlies emergent patterning of plumage in capuchino seedeaters

2022 ◽  
Vol 289 (1966) ◽  
Author(s):  
Cecilia Estalles ◽  
Sheela P. Turbek ◽  
María José Rodríguez-Cajarville ◽  
Luís Fábio Silveira ◽  
Kazumasa Wakamatsu ◽  
...  
Keyword(s):  
Animal Communication ◽  
The Body ◽  
Body Parts ◽  
Genetic Changes ◽  
Association Analyses ◽  
Colour Variation ◽  
Genomic Changes ◽  
Colour Patterns ◽  
Coloration Patterns ◽  
Genomic Regions

Coloration traits are central to animal communication; they often govern mate choice, promote reproductive isolation and catalyse speciation. Specific genetic changes can cause variation in coloration, yet far less is known about how overall coloration patterns—which involve combinations of multiple colour patches across the body—can arise and are genomically controlled. We performed genome-wide association analyses to link genomic changes to variation in melanin (eumelanin and pheomelanin) concentration in feathers from different body parts in the capuchino seedeaters, an avian radiation with diverse colour patterns despite remarkably low genetic differentiation across species. Cross-species colour variation in each plumage patch is associated with unique combinations of variants at a few genomic regions, which include mostly non-coding (presumably regulatory) areas close to known pigmentation genes. Genotype–phenotype associations can vary depending on patch colour and are stronger for eumelanin pigmentation, suggesting eumelanin production is tightly regulated. Although some genes are involved in colour variation in multiple patches, in some cases, the SNPs associated with colour changes in different patches segregate spatially. These results suggest that coloration patterning in capuchinos is generated by the modular combination of variants that regulate multiple melanogenesis genes, a mechanism that may have promoted this rapid radiation.

scholarly journals Genomic diversity of SARS-CoV-2 in Oxford during United Kingdom’s first national lockdown

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Altar M. Munis ◽  
Monique Andersson ◽  
Alexander Mobbs ◽  
Stephen C. Hyde ◽  
Deborah R. Gill
Keyword(s):  
Large Scale ◽  
Genomic Diversity ◽  
Viral Diversity ◽  
Host Immune System ◽  
Infection Rates ◽  
Short Term ◽  
Viral Genomes ◽  
The United Kingdom ◽  
Local Spread ◽  
Term Evolution

AbstractEpidemiological efforts to model the spread of SARS-CoV-2, the virus that causes COVID-19, are crucial to understanding and containing current and future outbreaks and to inform public health responses. Mutations that occur in viral genomes can alter virulence during outbreaks by increasing infection rates and helping the virus evade the host immune system. To understand the changes in viral genomic diversity and molecular epidemiology in Oxford during the first wave of infections in the United Kingdom, we analyzed 563 clinical SARS-CoV-2 samples via whole-genome sequencing using Nanopore MinION sequencing. Large-scale surveillance efforts during viral epidemics are likely to be confounded by the number of independent introductions of the viral strains into a region. To avoid such issues and better understand the selection-based changes occurring in the SARS-CoV-2 genome, we utilized local isolates collected during the UK’s first national lockdown whereby personal interactions, international and national travel were considerably restricted and controlled. We were able to track the short-term evolution of the virus, detect the emergence of several mutations of concern or interest, and capture the viral diversity of the region. Overall, these results demonstrate genomic pathogen surveillance efforts have considerable utility in controlling the local spread of the virus.

scholarly journals Lokale Anpassung bei Waldbaumarten: genetische Prozesse und Bedeutung im Klimawandel

2016 ◽  
Vol 167 (6) ◽  
pp. 333-340
Author(s):  
Christian Rellstab ◽  
Andrea R. Pluess ◽  
Felix Gugerli
Keyword(s):  
Local Adaptation ◽  
Environmental Gradients ◽  
Management Strategies ◽  
Environmental Parameters ◽  
Forest Trees ◽  
Local Conditions ◽  
Genetic Changes ◽  
Association Analyses ◽  
Temperature And Precipitation ◽  
Technological Advances

Local adaptation in forest trees: genetic processes and relevance under climate change Forest trees will have to adapt to future climatic changes, a process that will comprise genetic changes as a key component. Owing to technological advances it is now possible to identify the signature of natural selection and local adaptation in the genome. Environmental association analyses aim at associating adaptive genetic patterns with environmental parameters describing the local habitat. On the basis of such studies – including own investigations using oak and beech in Switzerland –, we show that forest trees are genetically differentiated along various environmental gradients, especially temperature and precipitation. Numerous genes could be found that presumably play a role in the adaptation to such environmental factors. Based on these findings, one could identify trees or stands that are adapted to future local conditions, and respective seed material could be considered in silviculture. Because such approaches are still in their infancy and because genome-environment interactions are complex, management strategies should focus on the preservation of (adaptive) genetic diversity, natural regeneration, and connectivity among stands. This would set the basis for the local adaptation of forest stands to altered environmental conditions by natural processes.

scholarly journals VERSO: a comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples

2020 ◽  
Author(s):  
Daniele Ramazzotti ◽  
Fabrizio Angaroni ◽  
Davide Maspero ◽  
Carlo Gambacorti-Passerini ◽  
Marco Antoniotti ◽  
...  
Keyword(s):  
Viral Evolution ◽  
Genomic Diversity ◽  
Contact Tracing ◽  
Sequencing Data ◽  
Spike Gene ◽  
Consensus Sequences ◽  
Viral Genomes ◽  
Variant Frequency ◽  
Algorithmic Strategy ◽  
Comprehensive Framework

SummaryWe introduce VERSO, a two-step framework for the characterization of viral evolution from sequencing data of viral genomes, which improves over phylogenomic approaches for consensus sequences. VERSO exploits an efficient algorithmic strategy to return robust phylogenies from clonal variant profiles, also in conditions of sampling limitations. It then leverages variant frequency patterns to characterize the intra-host genomic diversity of samples, revealing undetected infection chains and pinpointing variants likely involved in homoplasies. On simulations, VERSO outperforms state-of-the-art tools for phylogenetic inference. Notably, the application to 6726 Amplicon and RNA-seq samples refines the estimation of SARS-CoV-2 evolution, while co-occurrence patterns of minor variants unveil undetected infection paths, which are validated with contact tracing data. Finally, the analysis of SARS-CoV-2 mutational landscape uncovers a temporal increase of overall genomic diversity, and highlights variants transiting from minor to clonal state and homoplastic variants, some of which falling on the spike gene. Available at: https://github.com/BIMIB-DISCo/VERSO.

scholarly journals Yaravirus: A novel 80-nm virus infectingAcanthamoeba castellanii

2020 ◽  
Vol 117 (28) ◽  
pp. 16579-16586 ◽  
Author(s):  
Paulo V. M. Boratto ◽  
Graziele P. Oliveira ◽  
Talita B. Machado ◽  
Ana Cláudia S. P. Andrade ◽  
Jean-Pierre Baudoin ◽  
...  
Keyword(s):  
Major Capsid Protein ◽  
Amino Acid Level ◽  
Three Dimensional ◽  
Genomic Diversity ◽  
Phylogenetic Distance ◽  
Preliminary Assessment ◽  
Dna Viruses ◽  
Origin And Evolution ◽  
Viral Genomes ◽  
Jelly Roll

Here we report the discovery of Yaravirus, a lineage of amoebal virus with a puzzling origin and evolution. Yaravirus presents 80-nm-sized particles and a 44,924-bp dsDNA genome encoding for 74 predicted proteins. Yaravirus genome annotation showed that none of its genes matched with sequences of known organisms at the nucleotide level; at the amino acid level, six predicted proteins had distant matches in the nr database. Complimentary prediction of three-dimensional structures indicated possible function of 17 proteins in total. Furthermore, we were not able to retrieve viral genomes closely related to Yaravirus in 8,535 publicly available metagenomes spanning diverse habitats around the globe. The Yaravirus genome also contained six types of tRNAs that did not match commonly used codons. Proteomics revealed that Yaravirus particles contain 26 viral proteins, one of which potentially representing a divergent major capsid protein (MCP) with a predicted double jelly-roll domain. Structure-guided phylogeny of MCP suggests that Yaravirus groups together with the MCPs ofPleurochrysisendemic viruses. Yaravirus expands our knowledge of the diversity of DNA viruses. The phylogenetic distance between Yaravirus and all other viruses highlights our still preliminary assessment of the genomic diversity of eukaryotic viruses, reinforcing the need for the isolation of new viruses of protists.

Ability of urovysion FISH analysis to select patients with low- or intermediate-risk non-muscle-invasive bladder cancer (LI-NMIBC) for decreased surveillance.

2011 ◽  
Vol 29 (7_suppl) ◽  
pp. 283-283
Author(s):  
H. M. Rosevear ◽  
A. J. Lightfoot ◽  
M. A. O'Donnell
Keyword(s):  
First Year ◽  
Fish Analysis ◽  
Low Grade ◽  
High Grade ◽  
Genetic Changes ◽  
Screening Intervals ◽  
Muscle Invasive ◽  
Initial Resection

283 Background: Recurrent LI-NMIBC is difficult to detect cytologically, requiring frequent cystoscopies. Urovysion's (Abbot Laboratories, Downers Grove, IL) fluorescent in situ hybridization assay (FISH) detects genetic changes associated with LI-NMIBC and may be useful in identifying patients for extended screening intervals. Methods: Charts of 54 consecutive patients with LI-NMIBC who underwent cystoscopy, cytology, and FISH analysis every 3 months for the first year after resection since 2004 were retrospectively identified and reviewed. We analyzed the number of tumors or high-grade cytologies that would have been missed if surveillance cystoscopy, cytology, and FISH analysis had not been done between 3 and 12 months post-resection for patients with a normal cystoscopy, cytology, and FISH analysis at 3 months after initial resection and compared those results to patients with normal cystoscopy, cytology, and abnormal FISH analysis. Results: Mean age of the 54 patients was 67 (range 25–89) and 41 were males. Thirty-nine patients had normal cystoscopy, cytology, and FISH analysis at 3-months follow-up. If no further surveillance was done until 1 year post-resection, 2 low-grade tumors (3 and 7 mm at 7 months post-resection) and 2 incidents of high-grade cytology would have been missed (4 of 39, 10%). Fifteen patients had normal cystoscopy and cytology but abnormal FISH analysis results at 3 months. If no further surveillance had been done until 1 year after resection, 6 tumors (6 of 15, 40%) (5, 8, 3, 3, 9, 2 mm at 5, 6, 6, 7, 9, 10 months post-resection) and no high-grade cytology would have been missed. Overall, statistically fewer patients with normal compared to abnormal FISH analysis at first follow-up developed tumors before 1 year (4 of 39 vs. 6 of 15, p=0.033). Conclusions: FISH analysis can be used to significantly increase our ability to select patients suitable for extended screening intervals. It may be prudent to include FISH analysis at the first post-resection follow-up before selecting patients with LI-NMIBC for an extended screening interval. [Table: see text]

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