scholarly journals Evolutionary dynamics and geographic dispersal of beta coronaviruses in African bats

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10434
Author(s):  
Babatunde O. Motayo ◽  
Olukunle Oluwapamilerin Oluwasemowo ◽  
Paul A. Akinduti
Keyword(s):  
Evolutionary Dynamics ◽  
Evolutionary Rate ◽  
Sequence Data ◽  
Reservoir Host ◽  
South American ◽  
The Novel ◽  
Long Distance ◽  
Evolutionary Origins ◽  
Novel Coronavirus ◽  
African Bats

Bats have been shown to serve as reservoir host of various viral agents including coronaviruses. They have also been associated with the novel coronavirus SARS-CoV-2. This has made them an all important agent for CoV evolution and transmission. Our objective in this study was to investigate the dispersal, phylogenomics and evolution of betacoronavirus (βCoV) among African bats. We retrieved sequence data from established databases such as GenBank and Virus Pathogen Resource, covering the partial RNA dependent RNA polymerase (RdRP) gene of bat coronaviruses from eight African, three Asian, five European, two South American countries and Australia. We analyzed for phylogeographic information relating to genetic diversity and evolutionary dynamics. Our study revealed that majority of the African strains fell within Norbecovirus subgenera, with an evolutionary rate of 1.301 × 10−3, HPD (1.064 × 10−3–1.434 × 10−3) subs/site/year. The African strains diversified into three main subgenera, Norbecovirus, Hibecovirus and Merbecovirus. The time to most common recent ancestor for Norbecovirus strains was 1973, and 2007, for the African Merbecovirus strains. There was evidence of inter species transmission of Norbecovirus among bats in Cameroun and DRC. Phlylogeography showed that there were inter-continental spread of Bt-CoV from Europe, China and Hong Kong into Central and Southern Africa, highlighting the possibility of long distance transmission. Our study has elucidated the possible evolutionary origins of βCoV among African bats; we therefore advocate for broader studies of whole genome sequences of BtCoV to further understand the drivers for their emergence and zoonotic spillovers into human population.

scholarly journals Evolutionary Dynamics And Geographic Dispersal Of Beta Coronaviruses In African Bats

2020 ◽  
Author(s):  
Babatunde Olanrewaju Motayo ◽  
Olukunle Oluwapamilerin Oluwasemowo ◽  
Paul Akiniyi Akinduti
Keyword(s):  
Evolutionary Dynamics ◽  
Evolutionary Rate ◽  
Sequence Data ◽  
Reservoir Host ◽  
South American ◽  
The Novel ◽  
Long Distance ◽  
Evolutionary Origins ◽  
Novel Coronavirus ◽  
African Bats

ABSTRACTBats have been shown to serve as reservoir host of various viral agents including coronaviruses. They have also been associated with the novel coronavirus SARS-CoV-2. This has made them an all important agent for CoV evolution and transmission. Our objective in this study was to investigate the dispersal, phylogenomics and evolution of betacoronavirus (βCoV) among African bats. We retrieved sequence data from established databases such as GenBank and Virus Pathogen Resource, covering the partial RNA dependent RNA polymerase (RdRP) gene of Bat coronaviruses from eight African, three Asian, five European, two South American countries and Australia. We analyzed for Phylogeographic information relating to genetic diversity and evolutionary dynamics. Our study revealed that majority of the African strains fell within Norbecovirus subgenera, with an Evolutionary rate of 1.301 × 10−3, HPD (1.064 × 10−3 – 1.434 × 10−3) subs/site/year. The African strains diversified into three main subgenera, Norbecovirus, Hibecovirus and Marbecovirus. The time to most common recent ancestor for Norbecovirus strains was 1968, and 2010, for the African Marbecovirus strains. There was evidence of inter species transmission of Norbecovirus among bats in Cameroun and DRC. Phlylogeography showed that there were inter-continental spread of Bt-CoV from Europe, China and Hong Kong into Central and Southern Africa, highlighting the possibility of long distance transmission. Our study has elucidated the possible evolutionary origins of βCoV among African bats, we therefore advocate for broader studies of whole genome sequences of BtCoV to further understand the drivers for their emergence and zoonotic spillovers into human population.

scholarly journals Formulating a Scalable Approach to Patron-Requested Digitization in Archives

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Kevin S. Hawkins ◽  
Julie Judkins
Keyword(s):  
Risk Assessment ◽  
Copyright Law ◽  
The Novel ◽  
Long Distance ◽  
Novel Coronavirus ◽  
Distance Travel ◽  
Long Distance Travel

The novel coronavirus of 2019 (COVID-19) crisis has forced archives to rethink their modes of providing access to physical collections. Whereas difficult copyright questions raised by reproducing items could previously be skirted by requiring researchers to work with materials in person, the long-term closure of reading rooms and decrease in long-distance travel mean that archives need a workflow for handling user digitization requests that is scalable and requires consulting only easily identifiable information and, assuming full reproduction is off the table, reproducing items in a collection under 17 U.S.C. § 108 or through a strategy of rapid risk assessment. There is a challenge in creating a policy that will work across different formats and genres of archival materials, so this article offers some suggestions for how to think about these parameters according to US copyright law and calls for a committee of experts to work out a model policy that could serve remote users of archival collections even after the COVID-19 crisis has passed.

scholarly journals Early Phylogenetic Estimate Of The Effective Reproduction Number Of 2019-nCoV

2020 ◽  
Author(s):  
Alessia Lai ◽  
Annalisa Bergna ◽  
Carla Acciarri ◽  
Massimo Galli ◽  
Gianguglielmo Zehender
Keyword(s):  
Exponential Growth ◽  
Doubling Time ◽  
Evolutionary Dynamics ◽  
Evolutionary Rate ◽  
Reproduction Number ◽  
R Value ◽  
Phylogenetic Estimate ◽  
Novel Coronavirus ◽  
Birth Death

ABSTRACTTo reconstruct the evolutionary dynamics of the 2019 novel coronavirus, 52 2019-nCOV genomes available on 04 February 2020 at GISAID were analysed.The two models used to estimate the reproduction number (coalescent-based exponential growth and a birth-death skyline method) indicated an estimated mean evolutionary rate of 7.8 × 10−4 subs/site/year (range 1.1×10−4–15×10−4).The estimated R value was 2.6 (range 2.1-5.1), and increased from 0.8 to 2.4 in December 2019. The estimated mean doubling time of the epidemic was between 3.6 and 4.1 days.This study proves the usefulness of phylogeny in supporting the surveillance of emerging new infections even as the epidemic is growing.

scholarly journals Tracking and Classifying Global COVID-19 Cases by using 1D Deep Convolution Neural Networks

2020 ◽  
Author(s):  
Mark Amo-Boateng
Keyword(s):  
Neural Networks ◽  
Time Series ◽  
Time Series Data ◽  
Sequence Data ◽  
Series Data ◽  
The Novel ◽  
Response Curves ◽  
Convolution Neural Networks ◽  
Link Type ◽  
Novel Coronavirus

ABSTRACTThe novel coronavirus disease (COVID-19) and pandemic has taken the world by surprise and simultaneously challenged the health infrastructure of every country. Governments have resorted to draconian measures to contain the spread of the disease despite its devastating effect on their economies and education. Tracking the novel coronavirus 2019 disease remains vital as it influences the executive decisions needed to tighten or ease restrictions meant to curb the pandemic. One-Dimensional (1D) Convolution Neural Networks (CNN) have been used classify and predict several time-series and sequence data. Here 1D-CNN is applied to the time-series data of confirmed COVID-19 cases for all reporting countries and territories. The model performance was 90.5% accurate. The model was used to develop an automated AI tracker web app (AI Country Monitor) and is hosted on https://aicountrymonitor.org. This article also presents a novel concept of pandemic response curves based on cumulative confirmed cases that can be use to classify the stage of a country or reporting territory. It is our firm believe that this Artificial Intelligence COVID-19 tracker can be extended to other domains such as the monitoring/tracking of Sustainable Development Goals (SDGs) in addition to monitoring and tracking pandemics.

scholarly journals Mutations in SARS-CoV-2 Variants Modulate the Microscopic Dynamics of Neutralizing Antibodies

2021 ◽  
Author(s):  
Dhiman Ray ◽  
Riley Nicolas Quijano ◽  
Ioan Andricioaei
Keyword(s):  
Monoclonal Antibodies ◽  
Neutralizing Antibodies ◽  
Rational Design ◽  
Graph Connectivity ◽  
World Population ◽  
The Novel ◽  
Long Distance ◽  
Correlated Motion ◽  
Novel Coronavirus ◽  
Microscopic Dynamics

Monoclonal antibodies have emerged as viable treatment for the COVID-19 disease caused by the SARS-CoV-2 virus. But the new viral variants can reduce the efficacy of the currently available antibodies, as well as diminish the vaccine induced immunity. Here, we demonstrate how the microscopic dynamics of the SARS-CoV-2 neutralizing monoclonal antibodies, can be modulated by the mutations present in the spike proteins of the variants currently circulating in the world population. We show that the dynamical perturbation in the antibody structure can be diverse, depending both on the nature of the antibody and on the location of the mutation. The correlated motion between the antibody and the receptor binding domain (RBD) can also be changed, altering the binding affinity. By constructing a protein graph connectivity network, we could delineate the mutant induced modifications in the allosteric information flow pathway through the antibody, and observed the presence of both localized and long distance effects. We identified a loop consisting of residues 470-490 in the RBD which works like an anchor preventing the detachment of the antibodies, and individual mutations in that region can significantly affect the antibody binding propensity. Our study provides fundamental and atomistically detailed insight on how virus neutralization by monoclonal antibody can be impacted by the mutations in the epitope, and can potentially facilitate the rational design of monoclonal antibodies, effective against the new variants of the novel coronavirus.

scholarly journals BioLaboro: A bioinformatics system for detecting molecular assay signature erosion and designing new assays in response to emerging and reemerging pathogens

2020 ◽  
Author(s):  
Mitchell Holland ◽  
Daniel Negrón ◽  
Shane Mitchell ◽  
Nate Dellinger ◽  
Mychal Ivancich ◽  
...  
Keyword(s):  
In Silico ◽  
Sequence Data ◽  
Use Cases ◽  
Detection Accuracy ◽  
The Novel ◽  
Nucleoprotein Gene ◽  
Pcr Assays ◽  
Primer Sets ◽  
Novel Coronavirus ◽  
Pathogen Genome

AbstractBackgroundEmerging and reemerging infectious diseases such as the novel Coronavirus disease, COVID-19 and Ebola pose a significant threat to global society and test the public health community’s preparedness to rapidly respond to an outbreak with effective diagnostics and therapeutics. Recent advances in next generation sequencing technologies enable rapid generation of pathogen genome sequence data, within 24 hours of obtaining a sample in some instances. With these data, one can quickly evaluate the effectiveness of existing diagnostics and therapeutics using in silico approaches. The propensity of some viruses to rapidly accumulate mutations can lead to the failure of molecular detection assays creating the need for redesigned or newly designed assays.ResultsHere we describe a bioinformatics system named BioLaboro to identify signature regions in a given pathogen genome, design PCR assays targeting those regions, and then test the PCR assays in silico to determine their sensitivity and specificity. We demonstrate BioLaboro with two use cases: Bombali Ebolavirus (BOMV) and the novel Coronavirus 2019 (SARS-CoV-2). For the BOMV, we analyzed 30 currently available real-time reverse transcription-PCR assays against the three available complete genome sequences of BOMV. Only two met our in silico criteria for successful detection and neither had perfect matches to the primer/probe sequences. We designed five new primer sets against BOMV signatures and all had true positive hits to the three BOMV genomes and no false positive hits to any other sequence. Four assays are closely clustered in the nucleoprotein gene and one is located in the glycoprotein gene. Similarly, for the SARS-CoV-2, we designed five highly specific primer sets that hit all 145 whole genomes (available as of February 28, 2020) and none of the near neighbors.ConclusionsHere we applied BioLaboro in two real-world use cases to demonstrate its capability; 1) to identify signature regions, 2) to assess the efficacy of existing PCR assays to detect pathogens as they evolve over time, and 3) to design new assays with perfect in silico detection accuracy, all within hours, for further development and deployment. BioLaboro is designed with a user-friendly graphical user interface for biologists with limited bioinformatics experience.

scholarly journals The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India (Preprint)

2020 ◽  
Author(s):  
Anindita Banerjee ◽  
Rakesh Sarkar ◽  
Suvrotoa Mitra ◽  
Mahadeb Lo ◽  
Shanta Dutta ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Transmission Rate ◽  
Nonstructural Protein ◽  
Phylogenetic Analyses ◽  
Evolutionary Genetics ◽  
Nucleotide Sequences ◽  
Major Group ◽  
The Novel ◽  
Indian States ◽  
Novel Coronavirus

BACKGROUND The RNA genome of the emerging novel coronavirus is rapidly mutating, and its human-to-human transmission rate is increasing. Hence, temporal dissection of their evolutionary dynamics, the nature of variations among different strains, and understanding the single nucleotide polymorphisms in the endemic settings are crucial. Delineating the heterogeneous genomic constellations of this novel virus will help us understand its complex behavior in a particular geographical region. OBJECTIVE This is a comprehensive analysis of 95 Indian SARS-CoV-2 genome sequences available from the Global Initiative on Sharing All Influenza Data (GISAID) repository during the first 6 months of 2020 (January through June). Evolutionary dynamics, gene-specific phylogeny, and the emergence of the novel coevolving mutations in 9 structural and nonstructural genes among circulating SARS-CoV-2 strains across 12 different Indian states were analyzed. METHODS A total of 95 SARS-CoV-2 nucleotide sequences submitted from India were downloaded from the GISAID database. Molecular Evolutionary Genetics Analysis, version X software was used to construct the 9 phylogenetic dendrograms based on nucleotide sequences of the SARS-CoV-2 genes. Analyses of the coevolving mutations were done in comparison to the prototype SARS-CoV-2 from Wuhan, China. The secondary structure of the RNA-dependent RNA polymerase/nonstructural protein NSP12 was predicted with respect to the novel A97V mutation. RESULTS Phylogenetic analyses revealed the evolution of “genome-type clusters” and adaptive selection of “L”-type SARS-CoV-2 strains with genetic closeness to the bat severe acute respiratory syndrome–like coronaviruses. These strains were distant to pangolin or Middle East respiratory syndrome–related coronavirus strains. With regard to the novel coevolving mutations, 2 groups have been seen circulating in India at present, the “major group” (66/95, 69.4%) and the “minor group” (21/95, 22.1%) , harboring 4 and 5 coexisting mutations, respectively. The “major group” mutations fall in the A2a clade. All the minor group mutations, except 11083G>T (L37F, NSP6 gene), were unique to the Indian isolates. CONCLUSIONS This study highlights the rapidly evolving SARS-CoV-2 virus and the cocirculation of multiple clades and subclades. This comprehensive study is a potential resource for monitoring the novel mutations in the viral genome, interpreting changes in viral pathogenesis, and designing vaccines or other therapeutics.

scholarly journals The influence of floral variation and geographic disjunction on the evolutionary dynamics of Ronnbergia and Wittmackia (Bromeliaceae: Bromelioideae)

2019 ◽  
Vol 192 (4) ◽  
pp. 609-624
Author(s):  
Julián Aguirre-Santoro ◽  
Nelson R Salinas ◽  
Fabián A Michelangeli
Keyword(s):  
Atlantic Forest ◽  
Evolutionary Dynamics ◽  
Evolutionary Rate ◽  
Floral Evolution ◽  
Long Distance Dispersal ◽  
Long Distance ◽  
Floral Variation ◽  
The Pacific ◽  
The Caribbean ◽  
Forest C

Abstract The Ronnbergia alliance is a lineage of two genera, Ronnbergia and Wittmackia, which diversified in three centres of distribution; the Pacific Forest, the Atlantic Forest and the Caribbean. In this study, we reconstructed the most plausible biogeographic scenario that explain the disjunct evolution of the Ronnbergia alliance in these centres of diversity. We also compared the evolutionary rate dynamics of lineage diversification and floral evolution in each of these areas. Our results suggested that the Ronnbergia alliance originated in the Atlantic Forest c. 5.2 Mya. Ronnbergia originated c. 3.5 Mya after a long-distance dispersal event to the Pacific Forest. The diversification of Wittmackia started in the Atlantic Forest, c. 3.2 Mya, and experienced more heterogeneous evolutionary rate dynamics than Ronnbergia during its radiation. In Wittmackia a long-distance dispersal from the Atlantic Forest to Jamaica gave rise to the Caribbean clade, which diversified rapidly and experienced significantly higher rates of floral evolution. This study helped in understanding how bromeliad diversification occurs differently among major centres of biodiversity. In our case, we found how the Caribbean is a much more dynamic area of diversification than the Atlantic Forest or the Pacific Forest.

Ancient Vicariance or Recent Long‐Distance Dispersal? Inferences about Phylogeny and South American–African Disjunctions in Rapateaceae and Bromeliaceae Based on ndhF Sequence Data

2004 ◽  
Vol 165 (S4) ◽  
pp. S35-S54 ◽  
Author(s):  
Thomas J. Givnish ◽  
Kendra C. Millam ◽  
Timothy M. Evans ◽  
Jocelyn C. Hall ◽  
J. Chris Pires ◽  
...  
Keyword(s):  
Sequence Data ◽  
South American ◽  
Long Distance Dispersal ◽  
Long Distance

scholarly journals The novel Coronavirus enigma: Phylogeny and mutation analyses of SARS-CoV-2 viruses circulating in India during early 2020

2020 ◽  
Author(s):  
Anindita Banerjee ◽  
Rakesh Sarkar ◽  
Suvrotoa Mitra ◽  
Mahadeb Lo ◽  
Shanta Dutta ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Phylogenetic Analyses ◽  
Major Group ◽  
Phylogenetic Study ◽  
The Novel ◽  
Structural Genes ◽  
Adaptive Selection ◽  
Potential Resource ◽  
Novel Coronavirus ◽  
Genetic Closeness

AbstractBackgroundThis is a comprehensive analysis of 46 Indian SARS-CoV-2 genome sequences available from the NCBI and GISAID repository during early 2020. Evolutionary dynamics, gene-specific phylogeny and emergence of the novel co-evolving mutations in nine structural and non-structural genes among circulating SARS-CoV-2 strains in ten states of India have been assessed.Materials and methods46 SARS-CoV-2 nucleotide sequences submitted from India were downloaded from the GISAID (39/46) or from NCBI (7/46) database. Phylogenetic study and analyses of mutation were based on the nine structural and non-structural genes of SARS-CoV-2 strains. Secondary structure of RdRP/NSP12 protein was predicted with respect to the novel A97V mutation.ResultsPhylogenetic analyses revealed the evolution of “genome-type clusters” and adaptive selection of “L” type SARS-CoV-2 strains with genetic closeness to the bat SARS-like coronaviruses than pangolin or MERS-CoVs. With regards to the novel co-evolving mutations, 2 groups are seen to circulate in India at present: the “major group” (52.2%) and the “minor group” (30.4%), harboring four and five co-existing mutations, respectively. The “major group” mutations fall in the A2a clade. All the minor group mutations, except 11083G>T (L37F, NSP6) were unique to the Indian isolates.ConclusionThe study highlights rapidly evolving SARS-CoV-2 virus and co-circulation of multiple clades and sub-clades, driving this pandemic worldwide. This comprehensive study is a potential resource for monitoring the novel mutations in the viral genome, changes in viral pathogenesis, for designing vaccines and other therapeutics.

Sign in / Sign up

Export Citation Format

Share Document