Genetic Characterization of Betacoronavirus Lineage C Viruses in Bats Reveals Marked Sequence Divergence in the Spike Protein of Pipistrellus Bat Coronavirus HKU5 in Japanese Pipistrelle: Implications for the Origin of the Novel Middle East Respiratory Syndrome Coronavirus
Susanna K. P. Lau,Kenneth S. M. Li,Alan K.L. Tsang,Carol S. F. Lam,Shakeel Ahmed,Honglin Chen,Kwok-Hung Chan,Patrick C. Y. Woo,Kwok-Yung Yuen +8 more
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TLDR
Although MERS-CoV may have diverged from potential lineage C betacoronaviruses in European bats more recently, these bat viruses were unlikely to be the direct ancestor of Meredia respiratory syndrome coronavirus.Citations
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Origin and evolution of pathogenic coronaviruses
Jie Cui,Fang Li,Zhengli Shi +2 more
TL;DR: The viral factors that enabled the emergence of diseases such as severe acute respiratory syndrome and Middle East respiratory syndrome are explored and the diversity and potential of bat-borne coronaviruses are highlighted.
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COVID-19 infection: Origin, transmission, and characteristics of human coronaviruses
Muhammad Adnan Shereen,Muhammad Adnan Shereen,Suliman Khan,Abeer Kazmi,Nadia Bashir,Rabeea Siddique +5 more
TL;DR: The approaches for developing effective vaccines and therapeutic combinations to cope with this viral outbreak are discussed and the emergence and pathogenicity of COVID-19 infection and previous human coronaviruses severe acute respiratory syndrome coronavirus (SARS-CoV) and middle east respiratory virus (MERS- coV) is analyzed.
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Structure, Function, and Evolution of Coronavirus Spike Proteins.
TL;DR: This article reviews current knowledge about the structures and functions of coronavirus spike proteins, illustrating how the two S1 domains recognize different receptors and how the spike proteins are regulated to undergo conformational transitions.
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Coronaviruses - drug discovery and therapeutic options.
TL;DR: The epidemiology, virology, clinical features and current treatment strategies of SARS and MERS are summarized, and the discovery and development of new virus-based and host-based therapeutic options for CoV infections are discussed.
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Middle East Respiratory Syndrome Coronavirus: Another Zoonotic Betacoronavirus Causing SARS-Like Disease
Jasper Fuk-Woo Chan,Susanna K. P. Lau,Kelvin K. W. To,Vincent C.C. Cheng,Patrick C. Y. Woo,Kwok-Yung Yuen +5 more
TL;DR: Developing an effective camel MERS-CoV vaccine and implementing appropriate infection control measures may control the continuing epidemic.
References
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MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
Koichiro Tamura,Daniel S. Peterson,Nicholas Peterson,Glen Stecher,Masatoshi Nei,Sudhir Kumar +5 more
TL;DR: The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
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MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
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New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
Stéphane Guindon,Jean-François Dufayard,Vincent Lefort,Maria Anisimova,Wim Hordijk,Olivier Gascuel +5 more
TL;DR: A new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves and a new test to assess the support of the data for internal branches of a phylogeny are introduced.
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The Pfam protein families database
Marco Punta,Penny Coggill,Ruth Y. Eberhardt,Jaina Mistry,John Tate,Chris Boursnell,Ningze Pang,Kristoffer Forslund,Goran Ceric,Jody Clements,Andreas Heger,Liisa Holm,Erik L. L. Sonnhammer,Sean R. Eddy,Alex Bateman,Robert D. Finn +15 more
TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.
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BEAST: Bayesian evolutionary analysis by sampling trees
TL;DR: BEAST is a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree that provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions.