scholarly journals Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Science ◽  
2021 ◽  
pp. eabh2644 ◽  
Author(s):  
Nuno R. Faria ◽  
Thomas A. Mellan ◽  
Charles Whittaker ◽  
Ingra M. Claro ◽  
Darlan da S. Candido ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Genome Sequencing ◽  
Immune Evasion ◽  
Molecular Clock ◽  
Spike Protein ◽  
Dynamical Model ◽  
Mortality Data ◽  
Clock Analysis ◽  
Protection Against Infection ◽  
Molecular Clock Analysis

Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1, acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7–2.4-fold more transmissible, and that previous (non-P.1) infection provides 54–79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.

scholarly journals Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil

2021 ◽  
Author(s):  
Nuno R. Faria ◽  
Thomas A. Mellan ◽  
Charles Whittaker ◽  
Ingra M. Claro ◽  
Darlan da S. Candido ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Genome Sequencing ◽  
Immune Evasion ◽  
Protective Immunity ◽  
Spike Protein ◽  
Mortality Data ◽  
Previous Infection ◽  
Clock Analysis ◽  
Rapid Transmission ◽  
Molecular Clock Analysis

AbstractCases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite high levels of previous infection there. Through genome sequencing of viruses sampled in Manaus between November 2020 and January 2021, we identified the emergence and circulation of a novel SARS-CoV-2 variant of concern, lineage P.1, that acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around early November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.4–2.2 times more transmissible and 25-61% more likely to evade protective immunity elicited by previous infection with non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.One-Sentence SummaryWe report the evolution and emergence of a SARS-CoV-2 lineage of concern associated with rapid transmission in Manaus.

scholarly journals Complete Genomic Sequence of Human Coronavirus OC43: Molecular Clock Analysis Suggests a Relatively Recent Zoonotic Coronavirus Transmission Event

2005 ◽  
Vol 79 (3) ◽  
pp. 1595-1604 ◽  
Author(s):  
Leen Vijgen ◽  
Els Keyaerts ◽  
Elien Moës ◽  
Inge Thoelen ◽  
Elke Wollants ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Complete Genome ◽  
Recent Common Ancestor ◽  
Human Coronavirus ◽  
Transmission Event ◽  
Most Recent Common Ancestor ◽  
A Genome ◽  
Clock Analysis ◽  
Group 2 ◽  
Molecular Clock Analysis

ABSTRACT Coronaviruses are enveloped, positive-stranded RNA viruses with a genome of approximately 30 kb. Based on genetic similarities, coronaviruses are classified into three groups. Two group 2 coronaviruses, human coronavirus OC43 (HCoV-OC43) and bovine coronavirus (BCoV), show remarkable antigenic and genetic similarities. In this study, we report the first complete genome sequence (30,738 nucleotides) of the prototype HCoV-OC43 strain (ATCC VR759). Complete genome and open reading frame (ORF) analyses were performed in comparison to the BCoV genome. In the region between the spike and membrane protein genes, a 290-nucleotide deletion is present, corresponding to the absence of BCoV ORFs ns4.9 and ns4.8. Nucleotide and amino acid similarity percentages were determined for the major HCoV-OC43 ORFs and for those of other group 2 coronaviruses. The highest degree of similarity is demonstrated between HCoV-OC43 and BCoV in all ORFs with the exception of the E gene. Molecular clock analysis of the spike gene sequences of BCoV and HCoV-OC43 suggests a relatively recent zoonotic transmission event and dates their most recent common ancestor to around 1890. An evolutionary rate in the order of 4 × 10−4 nucleotide changes per site per year was estimated. This is the first animal-human zoonotic pair of coronaviruses that can be analyzed in order to gain insights into the processes of adaptation of a nonhuman coronavirus to a human host, which is important for understanding the interspecies transmission events that led to the origin of the severe acute respiratory syndrome outbreak.

Molecular clock analysis

2012 ◽  
pp. 362-380 ◽  
Author(s):  
Philippe Lemey ◽  
David Posada
Keyword(s):  
Molecular Clock ◽  
Clock Analysis ◽  
Molecular Clock Analysis

scholarly journals Root Digger: a root placement program for phylogenetic trees

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ben Bettisworth ◽  
Alexandros Stamatakis
Keyword(s):  
Phylogenetic Analysis ◽  
Markov Model ◽  
Molecular Clock ◽  
Phylogenetic Trees ◽  
Markov Models ◽  
Root Position ◽  
Clock Analysis ◽  
Confidence Value ◽  
Root Location ◽  
Molecular Clock Analysis

Abstract Background In phylogenetic analysis, it is common to infer unrooted trees. However, knowing the root location is desirable for downstream analyses and interpretation. There exist several methods to recover a root, such as molecular clock analysis (including midpoint rooting) or rooting the tree using an outgroup. Non-reversible Markov models can also be used to compute the likelihood of a potential root position. Results We present a software called which uses a non-reversible Markov model to compute the most likely root location on a given tree and to infer a confidence value for each possible root placement. We find that is successful at finding roots when compared to similar tools such as IQ-TREE and MAD, and will occasionally outperform them. Additionally, we find that the exhaustive mode of is useful in quantifying and explaining uncertainty in rooting positions. Conclusions can be used on an existing phylogeny to find a root, or to asses the uncertainty of the root placement. is available under the MIT licence at https://www.github.com/computations/root_digger.

Late Miocene eastwards transatlantic dispersal of flightless anchonine weevils (Coleoptera: Curculionidae: Molytinae)

Zootaxa ◽  
2021 ◽  
Vol 4952 (1) ◽  
pp. 55-70
Author(s):  
VASILY V. GREBENNIKOV ◽  
ROBERT S. ANDERSON
Keyword(s):  
Phylogenetic Analysis ◽  
Atlantic Ocean ◽  
Molecular Clock ◽  
Molecular Data ◽  
West African ◽  
The West ◽  
Incertae Sedis ◽  
Clock Analysis ◽  
Morphological And Molecular Data ◽  
Molecular Clock Analysis

The weevil genera Aethiopacorep Voisin and Titilayo Cristóvão & Lyal are the only native African members of the nearly pantropical and poorly known tribe Anchonini. All Anchonini are flightless, a trait likely limiting dispersal, yet these weevils are found on both sides of the Atlantic Ocean. A phylogenetic analysis of 79 terminals and 3248 aligned positions from one mitochondrial and two nuclear ribosomal fragments supports a clade of West African Anchonini nested within American Anchonini. As suggested by previous authors, the Asian genera Himalanchonus Zherikhin and Otibazo Morimoto do not form a clade with the tribe’s core, and along with Cycloterinus Kolbe, Euthycodes Pascoe, Leptanchonus Morimoto, Nepalanchonus Zherikhin, and Tanyomus Champion, are here removed from Anchonini and placed as Molytinae incertae sedis. So defined, the monophyletic tribe Anchonini contains 36 genus-group names, all but two denoting American taxa. Using molecular clock analysis, we estimate the separation of the West African Anchonini from its American sister at 9.5–5.2 million years ago (Ma). This date greatly postdates the Cretaceous opening of the Atlantic Ocean (about 100 Ma) and, therefore, evokes a single transatlantic dispersal to West Africa, likely by over-water rafting, leading to subsequent diversification. We postulate this to be the first documented eastwards crossing of the Atlantic Ocean by terrestrial non-volant arthropods based on morphological and molecular data. 

scholarly journals Molecular Evolution of Puumala Hantavirus

2001 ◽  
Vol 75 (23) ◽  
pp. 11803-11810 ◽  
Author(s):  
Tarja Sironen ◽  
Antti Vaheri ◽  
Alexander Plyusnin
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Evolution ◽  
Genetic Variants ◽  
Rna Virus ◽  
Puumala Virus ◽  
Genetic Lineages ◽  
Clock Analysis ◽  
Geographical Clustering ◽  
The Individual ◽  
Molecular Clock Analysis

ABSTRACT Puumala virus (PUUV) is a negative-stranded RNA virus in the genusHantavirus, family Bunyaviridae. In this study, detailed phylogenetic analysis was performed on 42 complete S segment sequences of PUUV originated from several European countries, Russia, and Japan, the largest set available thus far for hantaviruses. The results show that PUUV sequences form seven distinct and well-supported genetic lineages; within these lineages, geographical clustering of genetic variants is observed. The overall phylogeny of PUUV is star-like, suggesting an early split of genetic lineages. The individual PUUV lineages appear to be independent, with the only exception to this being the Finnish and the Russian lineages that are closely connected to each other. Two strains of PUUV-like virus from Japan form the most ancestral lineage diverging from PUUV. Recombination points within the S segment were searched for and evidence for intralineage recombination events was seen in the Finnish, Russian, Danish, and Belgian lineages of PUUV. Molecular clock analysis showed that PUUV is a stable virus, evolving slowly at a rate of 0.7 × 10−7 to 2.2 × 10−6 nt substitutions per site per year.

scholarly journals Investigating the Characteristics and Evolution of Apical Membrane Antigen 1 (AMA1) of Plasmodium sp. using Phylogenetic Approach in Searching for Drug Candidate

2020 ◽  
Author(s):  
Rizky Nurdiansyah ◽  
Kevin Nathanael Ramanto ◽  
Priscilla Jessica
Keyword(s):  
Phylogenetic Tree ◽  
Protein Evolution ◽  
Molecular Clock ◽  
Apical Membrane ◽  
Evolutionary Relationship ◽  
Protein Domain ◽  
Apical Membrane Antigen 1 ◽  
Apical Membrane Antigen ◽  
Clock Analysis ◽  
Molecular Clock Analysis

Malaria is an endemic disease caused by Plasmodium parasite with female Anopheles mosquitoes as a vector. With the increase of drug resistance Plasmodium emerging around the world, a new method should be devised against the spread of Plasmodium sp lineage. Protein evolution of  Plasmodium sp. can be an invaluable aid as an  input for rational drug design and immune-informatics methods based on the novel virulent gene that exists in these protozoa. Previously, we did data mining in the PlasmoDB database and found several proteins shared by Plasmodium, one of  them was the Apical Membrane Antigen 1 (AMA1). This protein was further analyzed for its characteristics and evolutionary properties. AMA1 protein sequences from human-infecting Plasmodium (P. falciparum, vivax, knowlesi, ovale, and malariae) and non-infectious (P. berghei, coatneyi, and cynomolgi) were retrieved from PlasmoDB. Maximum likelihood phylogenetic tree with molecular clock analysis was reconstructed from AMA1 sequences using MEGAX. Protein domain analysis was done using the INTERPRO server. Several domains that can induce protective immunity and vaccine target were found in AMA1 of those plasmodium, such as coiled-coil, disordered region, and signal peptide domain. Furthermore, molecular clock analysis showed a similar evolutionary rate between AMA1 protein in human-infecting and non-infectious Plasmodium. Interestingly, the phylogenetic tree showed a mixed cluster of human- infecting with non-infectious, indicating a unique evolutionary relationship between Plasmodium lineage. Thus, this information could be beneficial in developing the drug and vaccine for Plasmodium-related infection. Keywords: AMA1, drug target, protein domain, protein evolution, Plasmodium.

scholarly journals Geographic reconstruction of the SARS-CoV-2 outbreak in Lombardy (Italy) during the early phase

2020 ◽  
Author(s):  
Valeria Micheli ◽  
Sara Giordana Rimoldi ◽  
Francesca Romeri ◽  
Francesco Comandatore ◽  
Alessandro Mancon ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Phylogenetic Reconstruction ◽  
Epidemiological Surveillance ◽  
Patient Identification ◽  
Lombardy Region ◽  
The World ◽  
Clock Analysis ◽  
Large Clusters ◽  
Genome Assemblies ◽  
Molecular Clock Analysis

The circulation of SARS-CoV-2 in Italy has been dominated by two large clusters of outbreaks in Northern part of the peninsula, source of alarming and prolonged infections in Lombardy region, in Codogno and Bergamo areas especially. The aim of the study was to expand understanding on the circulation of SARS-CoV-2 in the affected Lombardy areas. To this purpose, twenty full length genomes were collected from patients addressing to several Lombard hospitals from February 20th to April 4th, 2020. The obtained genome assemblies, available on the GISAD database and performed at the Referral Center for COVID-19 diagnosis, identified 2 main monophyletic clades, containing 9 and 52 isolates, respectively. The molecular clock analysis estimated a clusters divergence approximately one month before the first patient identification, supporting the hypothesis that different SARS-CoV-2 strains spread all over the world at different time, but their presence became evident only in late February along with Italian epidemic emergence. Therefore, the epidemiological reconstruction carried out by this work highlights multiple inputs of the virus into its initial circulation in Lombardy Region. However, a phylogenetic reconstruction robustness will be improved when other genomic sequences will be available, in order to guarantee a complete epidemiological surveillance.

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