The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect

To explore the SARS-CoV-2 pandemic in Algeria, a dataset comprising ninety-five genomes originating from SARS-CoV-2 sampled from Algeria and other countries worldwide, from 24 December 2019, through 4 March 2021, was thoroughly examined. While performing a multi-component analysis regarding the Algerian outbreak, the toolkit of phylogenetic, phylogeographic, haplotype, and genomic analysis were effectively implemented. We estimated the Time to the Most Recent Common Ancestor (TMRCA) in reference to the Algerian pandemic and highlighted the multiple introductions of the disease and the missing data depicted in the transmission loop. In addition, we emphasized the significant role played by local and international travels in disease dissemination. Most importantly, we unveiled mutational patterns, the effect of unique mutations on corresponding proteins, and the relatedness regarding the Algerian sequences to other sequences worldwide. Our results revealed individual amino-acid replacements such as the deleterious replacement A23T in the orf3a gene in Algeria_EPI_ISL_418241. Additionally, a connection between Algeria_EPI_ISL_420037 and sequences originating from the USA was observed through a USA characteristic amino-acid replacement T1004I in the nsp3 gene, found in the aforementioned Algerian sequence. Similarly, successful tracing could be established, such as Algeria/G37318-8849/2020|EPI_ISL_766863, which was imported from Saudi Arabia during the pilgrimage. Lastly, we assessed the Algerian mitigation measures regarding disease containment using statistical analyses.

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The Algerian chapter of SARS-CoV-2 pandemic: An evolutionary, genetic, and epidemiological prospect of the first wave

10.1101/2020.11.19.20235135 ◽

2020 ◽

Author(s):

Safia Zeghbib ◽

Balázs Somogyi ◽

Brigitta Zana ◽

Gábor Kemenesi ◽

Róbert Herczeg ◽

...

Keyword(s):

Amino Acid ◽

Vaccine Development ◽

Genomic Analysis ◽

Amino Acid Replacement ◽

Mitigation Measures ◽

Contact Tracing ◽

Use Of Time ◽

Starting Point ◽

Evolutionary Genetic ◽

The Usa

AbstractTo explore the SARS-CoV-2 early pandemic in Algeria, a dataset comprising forty-three genomes originating from SARS-CoV-2 sampled from Algeria and other countries worldwide, from 24 December 2019 through 8 March 2020, of which, were thoroughly examined. While performing a multi-component analysis regarding the Algerian outbreak, the toolkit of phylogenetic, phylodynamic, haplotype analyses and genomic analysis were effectively implemented. We estimated the TMRCA in reference to the Algerian pandemic and highlighted both the introduction of the disease originating in France and the missing data depicted in the transmission loop. Most importantly, we unveiled mutational patterns, recombination events and the relatedness regarding the Algerian sequences to the dataset. Our results revealed the unique amino-acid replacement L129F in the orf3a gene in Algeria_EPI_ISL_418241. Additionally, a connection between Algeria_EPI_ISL_420037 and sequences originating from the USA was observed through a USA characteristic amino-acid replacement T1004I in the nsp3 gene, found in the aforementioned Algerian sequence. Lastly, we assessed the Algerian mitigation measures regarding disease containment using statistical analyses.Author summaryA novel human coronavirus, specifically SARS-CoV-2, emerged in China in late 2019. In Algeria, the contact tracing revealed the introduction of the disease originated in France, however, the intricate dynamics regarding the disease remain unexplored. In this study, we attempt to portray our perspective regarding the evolutionary, genetic and epidemiological aspects of the early pandemic in Algeria during the spring of 2020, through the use of time scaled phylogeny, phylodynamic and mutational pattern characterization and exploration. Additionally, we assessed the efficiency of the implemented mitigation measures using statistical analysis. The results supported the virus introduction from France and highlighted an Algerian characteristic amino-acid replacement in addition to a relatedness to the USA sequences. Moreover, we revealed an indirect contamination among the three sampled patients. Therefore, our analysis is a starting point for further investigations and emphasize the importance regarding intensive sequencing and genome exploration for mitigation measures implementation, and both drug and vaccine development.

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Detection of SARS-CoV-2 variant 501Y.V2 in Comoros Islands in January 2021

Wellcome Open Research ◽

10.12688/wellcomeopenres.16889.1 ◽

2021 ◽

Vol 6 ◽

pp. 192

Author(s):

Charles N. Agoti ◽

George Githinji ◽

Khadija S. Mohammed ◽

Arnold W. Lambisia ◽

Zaydah R. de Laurent ◽

...

Keyword(s):

Common Ancestor ◽

Control Strategies ◽

Close Association ◽

Genomic Data ◽

Recent Common Ancestor ◽

Major Infection ◽

Multiple Introductions ◽

Most Recent Common Ancestor ◽

The Indian Ocean ◽

Local Transmission

Background. Genomic data is key in understanding the spread and evolution of SARS-CoV-2 pandemic and informing the design and evaluation of interventions. However, SARS-CoV-2 genomic data remains scarce across Africa, with no reports yet from the Indian Ocean islands. Methods. We genome sequenced six SARS-CoV-2 positive samples from the first major infection wave in the Union of Comoros in January 2021 and undertook detailed phylogenetic analysis. Results. All the recovered six genomes classified within the 501Y.V2 variant of concern (also known as lineage B.1.351) and appeared to be from 2 sub-clusters with the most recent common ancestor dated 30th Oct-2020 (95% Credibility Interval: 06th Sep-2020 to 10th Dec-2020). Comparison of the Comoros genomes with those of 501Y.V2 variant of concern from other countries deposited into the GISAID database revealed their close association with viruses identified in France and Mayotte (part of the Comoros archipelago and a France, Overseas Department). Conclusions. The recovered genomes, albeit few, confirmed local transmission following probably multiple introductions of the SARS-CoV-2 501Y.V2 variant of concern during the Comoros’s first major COVID-19 wave. These findings demonstrate the importance of genomic surveillance and have implications for ongoing control strategies on the islands.

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Coronavirus GenBrowser for monitoring adaptive evolution and transmission of SARS-CoV-2

10.1101/2020.12.23.20248612 ◽

2020 ◽

Author(s):

Dalang Yu ◽

Xiao Yang ◽

Bixia Tang ◽

Yi-Hsuan Pan ◽

Jianing Yang ◽

...

Keyword(s):

Adaptive Evolution ◽

Common Ancestor ◽

Early Stage ◽

Lineage Tracing ◽

Recent Common Ancestor ◽

Multiple Introductions ◽

Most Recent Common Ancestor ◽

The World ◽

Beijing China ◽

Fast Access

AbstractCOVID-19 has widely spread across the world, and much research is being conducted on the causative virus SARS-CoV-2. To help control the infection, we developed the Coronavirus GenBrowser (CGB) to monitor the pandemic. CGB allows visualization and analysis of the latest viral genomic data. Distributed genome alignments and an evolutionary tree built on the existing subtree are implemented for easy and frequent updates. The tree-based data are compressed at a ratio of 2,760:1, enabling fast access and analysis of SARS-CoV-2 variants. CGB can effectively detect adaptive evolution of specific alleles, such as D614G of the spike protein, in their early stage of spreading. By lineage tracing, the most recent common ancestor, dated in early March 2020, of nine strains collected from six different regions in three continents was found to cause the outbreak in Xinfadi, Beijing, China in June 2020. CGB also revealed that the first COVID-19 outbreak in Washington State was caused by multiple introductions of SARS-CoV-2. To encourage data sharing, CGB credits the person who first discovers any SARS-CoV-2 variant. As CGB is developed with eight different languages, it allows the general public in many regions of the world to easily access pre-analyzed results of more than 132,000 SARS-CoV-2 genomes. CGB is an efficient platform to monitor adaptive evolution and transmission of SARS-CoV-2.

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Evolution of the Heme Peroxidases of Culicidae (Diptera)

Psyche A Journal of Entomology ◽

10.1155/2012/146387 ◽

2012 ◽

Vol 2012 ◽

pp. 1-6 ◽

Cited By ~ 2

Author(s):

Austin L. Hughes

Keyword(s):

Amino Acid ◽

Gene Duplication ◽

Common Ancestor ◽

Expression Patterns ◽

Amino Acid Level ◽

Recent Common Ancestor ◽

Amino Acid Sequence Level ◽

Most Recent Common Ancestor ◽

High Level ◽

Heme Peroxidases

Phylogenetic analysis of heme peroxidases (HPXs) of Culicidae and other insects revealed six highly conserved ancient HPX lineages, each of which originated by gene duplication prior to the most recent common ancestor (MRCA) of Hemimetabola and Holmetabola. In addition, culicid HPX7 and HPX12 arose by gene duplication after the MRCA of Culicidae and Drosophilidae, while HPX2 orthologs were not found in any other order analyzed except Diptera. Within Diptera, HPX2, HPX7, and HPX12 were relatively poorly conserved at the amino acid level in comparison to the six ancient lineages. The genome ofAnopheles gambiaeincluded genes ecoding five proteins (HPX10, HPX11, HPX13, HXP14, and HPX15) without ortholgs in other genomes analyzed. Overall, gene expression patterns did not seem to reflect phylogenetic relationships, but genes that evolved rapidly at the amino acid sequence level tended to have divergent expression patterns as well. The uniquely high level of duplication of HPXs inA. gambiaemay have played a role in coevolution with malaria parasites.

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Evolution and variation of 2019-novel coronavirus

10.1101/2020.01.30.926477 ◽

2020 ◽

Cited By ~ 9

Author(s):

Chenglong Xiong ◽

Lufang Jiang ◽

Yue Chen ◽

Qingwu Jiang

Keyword(s):

Amino Acid ◽

Substitution Rate ◽

Phylogenetic Trees ◽

Common Ancestor ◽

Nucleotide Substitution ◽

Genetic Distances ◽

Recent Common Ancestor ◽

Nucleotide Substitution Rate ◽

Most Recent Common Ancestor ◽

Novel Coronavirus

AbstractBackgroundThe current outbreak caused by novel coronavirus (2019-nCoV) in China has become a worldwide concern. As of 28 January 2020, there were 4631 confirmed cases and 106 deaths, and 11 countries or regions were affected.MethodsWe downloaded the genomes of 2019-nCoVs and similar isolates from the Global Initiative on Sharing Avian Influenza Database (GISAID and nucleotide database of the National Center for Biotechnology Information (NCBI). Lasergene 7.0 and MEGA 6.0 softwares were used to calculate genetic distances of the sequences, to construct phylogenetic trees, and to align amino acid sequences. Bayesian coalescent phylogenetic analysis, implemented in the BEAST software package, was used to calculate the molecular clock related characteristics such as the nucleotide substitution rate and the most recent common ancestor (tMRCA) of 2019-nCoVs.ResultsAn isolate numbered EPI_ISL_403928 showed different phylogenetic trees and genetic distances of the whole length genome, the coding sequences (CDS) of ployprotein (P), spike protein (S), and nucleoprotein (N) from other 2019-nCoVs. There are 22, 4, 2 variations in P, S, and N at the level of amino acid residues. The nucleotide substitution rates from high to low are 1·05 × 10−2 (nucleotide substitutions/site/year, with 95% HPD interval being 6.27 × 10−4 to 2.72 × 10−2) for N, 5.34 × 10−3 (5.10 × 10−4, 1.28 × 10−2) for S, 1.69 × 10−3 (3.94 × 10−4, 3.60 × 10−3) for P, 1.65 × 10−3 (4.47 × 10−4, 3.24 × 10−3) for the whole genome, respectively. At this nucleotide substitution rate, the most recent common ancestor (tMRCA) of 2019-nCoVs appeared about 0.253-0.594 year before the epidemic.ConclusionOur analysis suggests that at least two different viral strains of 2019-nCoV are involved in this outbreak that might occur a few months earlier before it was officially reported.

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In-frame seven amino-acid duplication in AIP arose over the last 3000 years, disrupts protein interaction and stability and is associated with gigantism

Acta Endocrinologica ◽

10.1530/eje-17-0293 ◽

2017 ◽

Vol 177 (3) ◽

pp. 257-266 ◽

Cited By ~ 8

Author(s):

Roberto Salvatori ◽

Serban Radian ◽

Yoan Diekmann ◽

Donato Iacovazzo ◽

Alessia David ◽

...

Keyword(s):

Pituitary Adenoma ◽

Amino Acid ◽

Protein Stability ◽

Protein Interactions ◽

Common Ancestor ◽

Recent Common Ancestor ◽

Interacting Protein ◽

Aryl Hydrocarbon ◽

Most Recent Common Ancestor ◽

The Uk

Objective Mutations in the aryl hydrocarbon receptor-interacting protein (AIP) gene are associated with pituitary adenoma, acromegaly and gigantism. Identical alleles in unrelated pedigrees could be inherited from a common ancestor or result from recurrent mutation events. Design and methods Observational, inferential and experimental study, including: AIP mutation testing; reconstruction of 14 AIP-region (8.3 Mbp) haplotypes; coalescent-based approximate Bayesian estimation of the time to most recent common ancestor (tMRCA) of the derived allele; forward population simulations to estimate current number of allele carriers; proposal of mutation mechanism; protein structure predictions; co-immunoprecipitation and cycloheximide chase experiments. Results Nine European-origin, unrelated c.805_825dup-positive pedigrees (four familial, five sporadic from the UK, USA and France) included 16 affected (nine gigantism/four acromegaly/two non-functioning pituitary adenoma patients and one prospectively diagnosed acromegaly patient) and nine unaffected carriers. All pedigrees shared a 2.79 Mbp haploblock around AIP with additional haploblocks privately shared between subsets of the pedigrees, indicating the existence of an evolutionarily recent common ancestor, the ‘English founder’, with an estimated median tMRCA of 47 generations (corresponding to 1175 years) with a confidence interval (9–113 generations, equivalent to 225–2825 years). The mutation occurred in a small tandem repeat region predisposed to slipped strand mispairing. The resulting seven amino-acid duplication disrupts interaction with HSP90 and leads to a marked reduction in protein stability. Conclusions The c.805_825dup allele, originating from a common ancestor, associates with a severe clinical phenotype and a high frequency of gigantism. The mutation is likely to be the result of slipped strand mispairing and affects protein–protein interactions and AIP protein stability.

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Allelic Genealogies in Sporophytic Self-Incompatibility Systems in Plants

Genetics ◽

10.1093/genetics/150.3.1187 ◽

1998 ◽

Vol 150 (3) ◽

pp. 1187-1198 ◽

Cited By ~ 9

Author(s):

Mikkel H Schierup ◽

Xavier Vekemans ◽

Freddy B Christiansen

Keyword(s):

Dominance Hierarchy ◽

Common Ancestor ◽

Recent Common Ancestor ◽

Self Incompatibility ◽

Most Recent Common Ancestor ◽

Dominance Interactions ◽

Turnover Process ◽

Neutral Gene ◽

Interspecific Comparisons ◽

Coalescence Times

Abstract Expectations for the time scale and structure of allelic genealogies in finite populations are formed under three models of sporophytic self-incompatibility. The models differ in the dominance interactions among the alleles that determine the self-incompatibility phenotype: In the SSIcod model, alleles act codominantly in both pollen and style, in the SSIdom model, alleles form a dominance hierarchy, and in SSIdomcod, alleles are codominant in the style and show a dominance hierarchy in the pollen. Coalescence times of alleles rarely differ more than threefold from those under gametophytic self-incompatibility, and transspecific polymorphism is therefore expected to be equally common. The previously reported directional turnover process of alleles in the SSIdomcod model results in coalescence times lower and substitution rates higher than those in the other models. The SSIdom model assumes strong asymmetries in allelic action, and the most recessive extant allele is likely to be the most recent common ancestor. Despite these asymmetries, the expected shape of the allele genealogies does not deviate markedly from the shape of a neutral gene genealogy. The application of the results to sequence surveys of alleles, including interspecific comparisons, is discussed.

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Molecular epidemiological characteristics of echovirus 6 in mainland China: extensive circulation of genotype F from 2007 to 2018

Archives of Virology ◽

10.1007/s00705-020-04934-7 ◽

2021 ◽

Author(s):

Wenjun Cheng ◽

Tianjiao Ji ◽

Shuaifeng Zhou ◽

Yong Shi ◽

Lili Jiang ◽

...

Keyword(s):

Common Ancestor ◽

Mainland China ◽

Recent Common Ancestor ◽

Genetic Characteristics ◽

Most Recent Common Ancestor ◽

Significant Difference ◽

Echovirus 6 ◽

Epidemiological Characteristics ◽

Highest Posterior Density ◽

Genotype F

AbstractEchovirus 6 (E6) is associated with various clinical diseases and is frequently detected in environmental sewage. Despite its high prevalence in humans and the environment, little is known about its molecular phylogeography in mainland China. In this study, 114 of 21,539 (0.53%) clinical specimens from hand, foot, and mouth disease (HFMD) cases collected between 2007 and 2018 were positive for E6. The complete VP1 sequences of 87 representative E6 strains, including 24 strains from this study, were used to investigate the evolutionary genetic characteristics and geographical spread of E6 strains. Phylogenetic analysis based on VP1 nucleotide sequence divergence showed that, globally, E6 strains can be grouped into six genotypes, designated A to F. Chinese E6 strains collected between 1988 and 2018 were found to belong to genotypes C, E, and F, with genotype F being predominant from 2007 to 2018. There was no significant difference in the geographical distribution of each genotype. The evolutionary rate of E6 was estimated to be 3.631 × 10-3 substitutions site-1 year-1 (95% highest posterior density [HPD]: 3.2406 × 10-3-4.031 × 10-3 substitutions site-1 year-1) by Bayesian MCMC analysis. The most recent common ancestor of the E6 genotypes was traced back to 1863, whereas their common ancestor in China was traced back to around 1962. A small genetic shift was detected in the Chinese E6 population size in 2009 according to Bayesian skyline analysis, which indicated that there might have been an epidemic around that year.

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The Ancestry of a Sample of Sequences Subject to Recombination

Genetics ◽

10.1093/genetics/151.3.1217 ◽

1999 ◽

Vol 151 (3) ◽

pp. 1217-1228 ◽

Cited By ~ 1

Author(s):

Carsten Wiuf ◽

Jotun Hein

Keyword(s):

Genetic Distance ◽

Population Size ◽

Upper Bound ◽

Recombination Rate ◽

Common Ancestor ◽

Recent Common Ancestor ◽

Sequence Length ◽

Most Recent Common Ancestor ◽

The Mean ◽

Mean Time

Abstract In this article we discuss the ancestry of sequences sampled from the coalescent with recombination with constant population size 2N. We have studied a number of variables based on simulations of sample histories, and some analytical results are derived. Consider the leftmost nucleotide in the sequences. We show that the number of nucleotides sharing a most recent common ancestor (MRCA) with the leftmost nucleotide is ≈log(1 + 4N Lr)/4Nr when two sequences are compared, where L denotes sequence length in nucleotides, and r the recombination rate between any two neighboring nucleotides per generation. For larger samples, the number of nucleotides sharing MRCA with the leftmost nucleotide decreases and becomes almost independent of 4N Lr. Further, we show that a segment of the sequences sharing a MRCA consists in mean of 3/8Nr nucleotides, when two sequences are compared, and that this decreases toward 1/4Nr nucleotides when the whole population is sampled. A measure of the correlation between the genealogies of two nucleotides on two sequences is introduced. We show analytically that even when the nucleotides are separated by a large genetic distance, but share MRCA, the genealogies will show only little correlation. This is surprising, because the time until the two nucleotides shared MRCA is reciprocal to the genetic distance. Using simulations, the mean time until all positions in the sample have found a MRCA increases logarithmically with increasing sequence length and is considerably lower than a theoretically predicted upper bound. On the basis of simulations, it turns out that important properties of the coalescent with recombinations of the whole population are reflected in the properties of a sample of low size.

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The evolutionary history and conservation value of disjunct Bartonia paniculata subsp. paniculata (Branched Bartonia) populations in Canada

Botany ◽

10.1139/cjb-2013-0063 ◽

2013 ◽

Vol 91 (9) ◽

pp. 605-613 ◽

Cited By ~ 6

Author(s):

Claudia Ciotir ◽

Chris Yesson ◽

Joanna Freeland

Keyword(s):

Great Lakes ◽

Evolutionary History ◽

Common Ancestor ◽

Recent Common Ancestor ◽

Great Lakes Region ◽

Conservation Value ◽

Most Recent Common Ancestor ◽

Disjunct Populations ◽

Management Plans ◽

Global Status

Understanding the spatial distribution of genetic diversity and its evolutionary history is an essential part of developing effective biodiversity management plans. This may be particularly true when considering the value of peripheral or disjunct populations. Although conservation decisions are often made with reference to geopolitical boundaries, many policy-makers also consider global distributions, and therefore a species’ global status may temper its regional status. Many disjunct populations can be found in the Great Lakes region of North America, including those of Bartonia paniculata subsp. paniculata, a species that has been designated as threatened in Canada but globally secure. We compared chloroplast sequences between disjunct (Canada) and core (USA) populations of B. paniculata subsp. paniculata separated by 600 km, which is the minimum distance between disjunct and core populations in this subspecies. We found that although lineages within the disjunct populations shared a relatively recent common ancestor, the genetic divergence between plants from Ontario and New Jersey was substantially greater than expected for a consubspecific comparison. A coalescence-based analysis dated the most recent common ancestor of the Canadian and US populations at approximately 534 000 years ago with the lower confidence estimate at 226 000 years ago. This substantially predates the Last Glacial Maximum and suggests that disjunct and core populations have followed independent evolutionary trajectories throughout multiple glacial–interglacial cycles. Our findings provide important insight into the diverse processes that have resulted in numerous disjunct species in the Great Lakes region and highlight a need for additional work on Canadian B. paniculata subsp. paniculata taxonomy prior to a reevaluation of its conservation value.

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