scholarly journals Molecular Epidemiology Surveillance of SARS-Cov-2: Mutations and Genetic Diversity One Year After Emerging

2021 ◽  
Author(s):  
Alejandro Flores-Alanis ◽  
Armando Cruz-Rangel ◽  
Flor Rodríguez-Gómez ◽  
James González ◽  
Carlos Alberto Torres-Guerrero ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genomic Analysis ◽  
Viral Fitness ◽  
Spike Protein ◽  
Molecular Surveillance ◽  
Low Genetic Diversity ◽  
Geographical Regions ◽  
Frequent Mutations ◽  
One Year ◽  
Over Time

In December 2019, the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the province of Wuhan, China. Since then, it has spread worldwide with new mutations being reported. We performed genomic analysis to identify the changes in genetic diversity of SARS-CoV-2 between December 2019 and November 2020, and through molecular surveillance, we monitored the mutations that could be involved in viral fitness. We analyzed 2,213 complete genomes from 6 geographical regions worldwide, which were downloaded from GenBank and GISAID databases. Although SARS-CoV-2 presented low genetic diversity, there has been an increase over time, with the presence of several hotspot mutations throughout its genome. We identified 7 frequent mutations that resulted in non-synonymous substitutions (dN). Two of them, C14408T>P323L and A23403G>D614G, located in the nsp12 and Spike protein, respectively, emerged early in the pandemic and showed a considerable increase in frequency over time. Two other mutations, A1163T>I120F in nsp2 and G22992A>S477N in the Spike protein emerged recently and have spread in Oceania and Europe. Continuous molecular surveillance of SARS-CoV-2 will be necessary to detect and describe the transmission dynamics of new variants of the virus with clinical relevance. This information is important to improve programs to control the virus.

scholarly journals Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 184
Author(s):  
Alejandro Flores-Alanis ◽  
Armando Cruz-Rangel ◽  
Flor Rodríguez-Gómez ◽  
James González ◽  
Carlos Alberto Torres-Guerrero ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Spike Protein ◽  
The Novel ◽  
Molecular Surveillance ◽  
Low Genetic Diversity ◽  
Geographical Regions ◽  
Frequent Mutations ◽  
One Year ◽  
The City ◽  
Over Time

In December 2019, the first cases of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified in the city of Wuhan, China. Since then, it has spread worldwide with new mutations being reported. The aim of the present study was to monitor the changes in genetic diversity and track non-synonymous substitutions (dN) that could be implicated in the fitness of SARS-CoV-2 and its spread in different regions between December 2019 and November 2020. We analyzed 2213 complete genomes from six geographical regions worldwide, which were downloaded from GenBank and GISAID databases. Although SARS-CoV-2 presented low genetic diversity, there has been an increase over time, with the presence of several hotspot mutations throughout its genome. We identified seven frequent mutations that resulted in dN substitutions. Two of them, C14408T>P323L and A23403G>D614G, located in the nsp12 and Spike protein, respectively, emerged early in the pandemic and showed a considerable increase in frequency over time. Two other mutations, A1163T>I120F in nsp2 and G22992A>S477N in the Spike protein, emerged recently and have spread in Oceania and Europe. There were associations of P323L, D614G, R203K and G204R substitutions with disease severity. Continuous molecular surveillance of SARS-CoV-2 will be necessary to detect and describe the transmission dynamics of new variants of the virus with clinical relevance. This information is important to improve programs to control the virus.

Genome typing and epidemiology of human listeriosis in New Zealand 1999-2018

2021 ◽  
Author(s):  
Lucia Rivas ◽  
Shevaun Paine ◽  
Pierre-Yves Dupont ◽  
Audrey Tiong ◽  
Beverley Horn ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
New Zealand ◽  
Epidemiological Data ◽  
Common Source ◽  
Snp Analysis ◽  
Whole Genome ◽  
Single Nucleotide ◽  
Low Genetic Diversity ◽  
Geographical Regions ◽  
Sequence Types

This study describes the epidemiology of listeriosis in New Zealand (NZ) between 1999 and 2018, as well as the retrospective whole genome sequencing (WGS) of 453 Listeria monocytogenes isolates corresponding to 95% of the human cases within this period. The average notified rate of listeriosis was 0.5 cases per 100,000 population and non-pregnancy associated cases were more prevalent than pregnancy-associated cases (average 19 and 5 cases per annum, respectively). Analysis of WGS data was assessed using multi-locus sequencing typing (MLST), including core-genome and whole-genome MLST (cgMLST and wgMLST) and single-nucleotide polymorphism (SNP) analysis. Thirty-nine sequence types (STs) were identified, with the most common being, ST1 (21.9%), ST4 (13.2%), ST2 (11.3%), ST120 (6.1%) and ST155 (6.4%). A total of 291 different cgMLST types were identified, with the majority (n = 243) of types observed as a single isolate, consistent with the observation that listeriosis is predominately sporadic. Amongst the 49 cgMLST types containing two or more isolates, 18 cgMLST types contained 2-4 isolates (50 isolates in total, including three outbreak-associated isolates) that shared low genetic diversity (0-2 whole-genome alleles), some of which were dispersed in time or geographical regions. SNP-analysis also produced comparable results to wgMLST. The low genetic diversity within these clusters suggests a potential common source but incomplete epidemiological data impaired retrospective epidemiological investigations. Prospective use of WGS analysis, together with thorough exposure information from cases will potentially identify future outbreaks more rapidly and possibly those that have been undetected for some time over different geographically regions.

Genetic consequences of long-term isolation for the last French population of Eryngium viviparum (Apiaceae)

2019 ◽  
Vol 191 (2) ◽  
pp. 285-298 ◽  
Author(s):  
Pauline Rascle ◽  
Elodie Flaven ◽  
Frédéric Bioret ◽  
Sylvie Magnanon ◽  
Erwan Glemarec ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Conservation Status ◽  
Disjunct Distribution ◽  
French Population ◽  
Endemic Plant ◽  
Evolutionary Potential ◽  
The North ◽  
Low Genetic Diversity ◽  
Geographical Regions ◽  
Seasonally Flooded

Abstract Eryngium viviparum (Apiaceae) is an endangered endemic plant of the Atlantic region of Europe, growing in seasonally flooded sites, and is characterized by a highly disjunct distribution. It occurs in just a few sites in the north-western part of the Iberian Peninsula and in a single locality in France. To improve the conservation status of E. viviparum in France, a conservation programme has been implemented to reintroduce the species. Before considering such an operation, genetic studies were conducted to determine the genetic status of the last French population and to identify the genetic source that should be considered for the best reintroduction strategy. Using microsatellite markers, we documented the genetic structure of the last French population and compared its genetic diversity with that of ten Iberian populations, which cover the three geographical regions where the species occurs. As expected, the French population of E. viviparum shows low genetic diversity due to a bottleneck and geographical isolation. The evolutionary potential appears low, with no private alleles in this population. Furthermore, this population is highly differentiated from the Iberian populations in terms of genetic variation and ecological niche. These results bring new questions regarding the conservation of E. viviparum in France, especially for management and reintroduction aimed at favouring genetic diversity and avoiding extinction.

First genomic analysis of the broad-host-range Rhizobium sp. LPU83 strain, a member of the low-genetic diversity Oregon-like Rhizobium sp. group

2011 ◽  
Vol 155 (1) ◽  
pp. 3-10 ◽  
Author(s):  
Gonzalo Torres Tejerizo ◽  
María Florencia Del Papa ◽  
Walter Draghi ◽  
Mauricio Lozano ◽  
María de los Ángeles Giusti ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Host Range ◽  
Genomic Analysis ◽  
Broad Host Range ◽  
Low Genetic Diversity ◽  
Rhizobium Sp

Genetic Diversity Within and Among Populations of Shorea Robusta Roxb. Ex Gaertn. In Bangladesh and Its Implications for Conservation

2021 ◽  
Vol 50 (2) ◽  
pp. 405-412
Author(s):  
Pragga Saha Sharmi ◽  
Md Abul Kashem ◽  
Rifat Samad ◽  
Mohammad Zabed Hossain
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Isolation By Distance ◽  
Genetic Erosion ◽  
Mantel Test ◽  
Small Population ◽  
Deciduous Forests ◽  
Shorea Robusta ◽  
Low Genetic Diversity ◽  
Geographical Regions

Fragmentation and reduction of natural population size render threats to the conservation of forest resources through depletion of genetic diversity. Hence, information on genetic structure of Sal (Shorea robusta Roxb. ex Gaertn.) populations is relevant for proper management and conservation of the tropical deciduous forests. The present study focused on assessing the genetic diversity of the populations of Sal which was the dominant tree species of the deciduous forests of Bangladesh. Plant leaf samples were collected from the three populations of Sal distributed in the three geographical regions including Madhupur tract in the districts Tangail and Gazipur and that of the districts of Cumilla and Dinajpur. DNA band profiles were generated using eight ISSR primers for a total of 13 samples taken from the three populations. Statistical analysis was done using PopGen 32 and GenAlEx 6.5 softwares. Principal coordinate analysis done on the DNA band profiles revealed that Sal populations of Madhupur tract and Cumilla positioned nearby while Dinajpur showed maximum genetic distance with that of Cumilla. Mantel test showed significant (p=0.05) correlation between genetic and geographic distances indicating “Isolation by Distance”. Data of the present study indicated higher genetic polymorphism (68.87%) in the Sal population of Madhupur tract compared to other two populations. Small population size of Sal of Dinajpur forest might be related with its low genetic diversity. Data of the present study suggest immediate attention for the conservation of Sal forests in Bangladesh before further genetic erosion occurs. Bangladesh J. Bot. 50(2): 405-412, 2021 (June)

scholarly journals Plasmodium falciparum Genetic Diversity in Panamá Based on glurp, msp-1 and msp-2 Genes: Implications for Malaria Elimination in Mesoamerica

Life ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 319
Author(s):  
Ana María Santamaría ◽  
Vanessa Vásquez ◽  
Chystrie Rigg ◽  
Dianik Moreno ◽  
Luis Romero ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Malaria Elimination ◽  
Multiple Correspondence Analysis ◽  
Strong Association ◽  
Parasite Load ◽  
Molecular Surveillance ◽  
Disease Propagation ◽  
Low Genetic Diversity ◽  
Imported Cases ◽  
Endemic Areas

Panamá, together with all the nations in Mesoamerica, has committed to eliminate malaria from the region by 2020. As these countries approach malaria elimination and local transmission decreases, an active molecular surveillance to identify genotypes circulating along the border areas is particularly needed to accurately infer infection origin, drug resistance and disease propagation patterns in the region. This study evaluated the genetic diversity and allele frequencies of msp-1, msp-2 and glurp genes using different molecular analyses (nested PCR, PCR-restriction fragment length polymorphism (RFLP) and sequencing) from 106 autochthonous and imported P. falciparum isolates collected from different endemic areas in Panamá between 2003 and 2019. We also explored if P. falciparum genotypes assessed with these molecular markers were associated with relevant malaria epidemiological parameters using a multiple correspondence analysis. A strong association of certain local haplotypes with their geographic distribution in endemic areas, but also with parasite load and presence of gametocytes, was evidenced. Few multiclonal infections and low genetic diversity among locally transmitted P. falciparum samples were detected, consequent with the low transmission intensity of this parasite in Panamá, a pattern likely to be extended across Mesoamerica. In addition, several imported cases were genetically dissimilar to local infections and representative of more diverse extra-continental lineages.

scholarly journals Low genetic diversity in Wolbachia-Infected Culex quinquefasciatus (Diptera: Culicidae) from Brazil and Argentina

2012 ◽  
Vol 54 (6) ◽  
pp. 325-329 ◽  
Author(s):  
Sirlei Antunes Morais ◽  
Fábio de Almeida ◽  
Lincoln Suesdek ◽  
Mauro Toledo Marrelli
Keyword(s):  
Genetic Diversity ◽  
Culex Quinquefasciatus ◽  
Southern Brazil ◽  
Human Pathogens ◽  
Nuclear Markers ◽  
Low Genetic Diversity ◽  
Geographical Regions ◽  
Filarial Nematodes ◽  
Wolbachia Endosymbiont ◽  
Mtdna Diversity

Culex quinquefasciatus is a vector of human pathogens, including filarial nematodes and several viruses. Although its epidemiological relevance is known to vary across geographical regions, an understanding of its population genetic structure is still incipient. In light of this, we evaluated the genetic diversity of Cx. quinquefasciatus and Cx. pipiens x Cx. quinquefasciatus hybrids collected from nine localities in Brazil and one site in Argentina. We used mitochondrial genes cox1 and nd4, along with the coxA and wsp genes of the maternally-inherited Wolbachia endosymbiont. The nd4 fragment was invariant between samples, whilst cox1 exhibited four haplotypes that separated two types of Cx. quinquefasciatus, one clustered in southern Brazil. Low sequence diversity was generally observed, being discussed. Both Brazilian and Argentinian mosquitoes were infected with a single Wolbachia strain. As reported in previous studies with these populations, cox1 and nd4 diversity is not congruent with the population structure revealed by nuclear markers or alar morphology. Future Cx. quinquefasciatus research should, if possible, evaluate mtDNA diversity in light of other markers.

scholarly journals Increased Genetic Diversity via Gene Flow Provides Hope for Acacia whibleyana, an Endangered Wattle Facing Extinction

Diversity ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 299
Author(s):  
Colette Blyth ◽  
Matthew J. Christmas ◽  
Doug C. Bickerton ◽  
Renate Faast ◽  
Jasmin G. Packer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
South Australia ◽  
Genomic Analysis ◽  
Unknown Origin ◽  
Genetic Connectivity ◽  
Conservation Genomics ◽  
Low Genetic Diversity ◽  
Pollinator Community ◽  
Management Recommendations

In this paper we apply a conservation genomics approach to make evidence-based management recommendations for Acacia whibleyana, an endangered shrub endemic to Eyre Peninsula, South Australia. We used population genomic analysis to assess genetic connectivity, diversity, and historical inbreeding across all known stands of the species sampling remnant stands, revegetated stands of unknown origin, and a post-fire seedling cohort. Our results indicate a degree of historical connectivity across the landscape, but habitat loss and/or pollinator community disruption are potential causes of strong genetic structure across the remnant stands. Remnant stands had low genetic diversity and showed evidence of historical inbreeding, but only low levels of intra-stand relatedness indicating that risks of contemporary inbreeding are low. Analysis of a post-fire first generation cohort of seedlings showed they likely resulted from intra-stand matings, resulting in reduced genetic diversity compared to the parents. However, admixed seedlings in this cohort showed an increase in heterozygosity relative to likely sources and the non-admixed seedlings of the same stand. Assisted inter-stand gene flow may prove an effective management strategy to boost heterozygosity and corresponding increases in adapting capacity in this endangered species.

scholarly journals Genetic diversity and evolution of SARS-CoV-2 in Belgium during the first wave outbreak

2021 ◽  
Author(s):  
Tony Wawina-Bokalanga ◽  
Joan Marti-Carreras ◽  
Bert Vanmechelen ◽  
Mandy Bloemen ◽  
Elke Wollants ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Geographic Distribution ◽  
Causative Agent ◽  
Synonymous Mutations ◽  
Data Analyses ◽  
Intervention Measures ◽  
Functional Implications ◽  
Variant Analysis ◽  
One Year ◽  
Over Time

SARS-CoV-2, the causative agent of COVID-19 was first detected in Belgium on 3rd February 2020, albeit the first epidemiological wave started in March and ended in June 2020. One year after the first epidemiological wave hit the country data analyses reveled the temporal and variant distribution of SARS-CoV-2 and its implication with Belgian epidemiological measures. In this study, 766 complete SARS-CoV-2 genomes of samples originating from the first epidemiological were sequenced to characterize the temporal and geographic distribution of the COVID-19 pandemic in Belgium through phylogenetic and variant analysis. Our analysis reveals the presence of the major circulating SARS-CoV-2 clades (G, GH and GR) and lineages circulating in Belgium at that time. Moreover, it contextualizes the density of SARS-CoV-2 cases over time with non-intervention measures taken to prevent the spread of SARS-CoV-2 in Belgium, specific international case imports and the functional implications of the most representative non-synonymous mutations present in Belgium between February to June 2020.

scholarly journals Development and Characterization of High-Throughput EST-Based SSR Markers for Pogostemon cablin Using Transcriptome Sequencing

Molecules ◽  
2018 ◽  
Vol 23 (8) ◽  
pp. 2014 ◽  
Author(s):  
Puyue Ouyang ◽  
Dali Kang ◽  
Xiaolu Mo ◽  
Enwei Tian ◽  
Yanyu Hu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Polymorphism Analysis ◽  
Large Set ◽  
Pogostemon Cablin ◽  
Geographical Regions ◽  
Molecular Assisted Selection ◽  
Diversity Studies

Simple sequence repeats (SSRs) or microsatellite markers derived from expressed sequence tags (ESTs) are routinely used for molecular assisted-selection breeding, comparative genomic analysis, and genetic diversity studies. In this study, we investigated 54,546 ESTs for the identification and development of SSR markers in Pogostemon cablin (Patchouli). In total, 1219 SSRs were identified from 1144 SSR-containing ESTs. Trinucleotides (80.8%) were the most abundant SSRs, followed by di- (10.8%), mono- (7.1%), and hexa-nucleotides (1.3%). The top six motifs were CCG/CGG (15.3%), AAG/CTT (15.0%), ACC/GGT (13.5%), AGG/CCT (12.4%), ATC/ATG (9.9%), and AG/CT (9.8%). On the basis of these SSR-containing ESTs, a total of 192 primer pairs were randomly designed and used for polymorphism analysis in 38 accessions collected from different geographical regions of Guangdong, China. Of the SSR markers, 45 were polymorphic and had allele variations from two to four. Furthermore, a transferability analysis of these primer pairs revealed a 10–40% cross-species transferability in 10 related species. This report is the first comprehensive study on the development and analysis of a large set of SSR markers in P. cablin. These markers have the potential to be used in quantitative trait loci mapping, genetic diversity studies, and the fingerprinting of cultivars of P. cablin.

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