Population Genomics Insights into the First Wave of COVID-19

Genomic diversity of SARS-CoV-2 in Coronavirus Disease 2019 patients

(2020) Zijie Shen et al.   CLINICAL INFECTIOUS DISEASES

Evolutionary history, potential intermediate animal host, and cross‐species analyses of SARS‐CoV‐2

(2020) Xingguang Li et al.   JOURNAL OF MEDICAL VIROLOGY

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

(2020) Roujian Lu et al.   LANCET

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

(2020) Chaolin Huang et al.   LANCET

First Case of 2019 Novel Coronavirus in the United States

(2020) Michelle L. Holshue et al.   NEW ENGLAND JOURNAL OF MEDICINE

A Novel Coronavirus from Patients with Pneumonia in China, 2019

(2020) Na Zhu et al.   NEW ENGLAND JOURNAL OF MEDICINE

The global spread of 2019-nCoV: a molecular evolutionary analysis

(2020) Domenico Benvenuto et al.   Pathogens and Global Health

The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

(2020)   Nature Microbiology

Characterization of the receptor-binding domain (RBD) of 2019 novel coronavirus: implication for development of RBD protein as a viral attachment inhibitor and vaccine

(2020) Wanbo Tai et al.   Cellular & Molecular Immunology

Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event

(2020) D. Paraskevis et al.   INFECTION GENETICS AND EVOLUTION

Bayesian phylodynamic inference on the temporal evolution and global transmission of SARS-CoV-2

(2020) Jianguo Li et al.   JOURNAL OF INFECTION

Computational Inference of Selection Underlying the Evolution of the Novel Coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2

(2020) Rachele Cagliani et al.   JOURNAL OF VIROLOGY

The proximal origin of SARS-CoV-2

(2020) Kristian G. Andersen et al.   NATURE MEDICINE

SARS-CoV-2 (COVID-19) by the numbers

(2020) Yinon M Bar-On et al.   eLife

Emergence of SARS-CoV-2 through recombination and strong purifying selection

(2020) Xiaojun Li et al.   Science Advances

Structural elucidation of SARS-CoV-2 vital proteins: Computational methods reveal potential drug candidates against main protease, Nsp12 polymerase and Nsp13 helicase

(2020) Muhammad Usman Mirza et al.   Journal of Pharmaceutical Analysis

A palindromic RNA sequence as a common breakpoint contributor to copy-choice recombination in SARS-COV-2

(2020) William R. Gallaher   ARCHIVES OF VIROLOGY

SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies

(2020) Timokratis Karamitros et al.   JOURNAL OF CLINICAL VIROLOGY

Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and Infection Clusters

(2020) Qi Liu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants

(2020) Bethany Dearlove et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Next-Generation Sequencing of Infectious Pathogens

(2019) Marta Gwinn et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica)

(2019) Ping Liu et al.   Viruses-Basel

Bioinformatics and functional analyses of coronavirus nonstructural proteins involved in the formation of replicative organelles

(2016) Benjamin W. Neuman   ANTIVIRAL RESEARCH

Extensive Positive Selection Drives the Evolution of Nonstructural Proteins in Lineage C Betacoronaviruses

(2016) Diego Forni et al.   JOURNAL OF VIROLOGY

Recombination in viruses: Mechanisms, methods of study, and evolutionary consequences

(2015) Marcos Pérez-Losada et al.   INFECTION GENETICS AND EVOLUTION

SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes

(2013) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Isolation of a Novel Coronavirus from a Man with Pneumonia in Saudi Arabia

(2012) Ali M. Zaki et al.   NEW ENGLAND JOURNAL OF MEDICINE

abc: an R package for approximate Bayesian computation (ABC)

(2012) Katalin Csilléry et al.   Methods in Ecology and Evolution

Recombination between Poliovirus and Coxsackie A Viruses of Species C: A Model of Viral Genetic Plasticity and Emergence

(2011) Nicolas Combelas et al.   Viruses-Basel

msABC: a modification of Hudson’s ms to facilitate multi-locus ABC analysis

(2010) P. PAVLIDIS et al.   Molecular Ecology Resources

Approximate Bayesian Computation (ABC) in practice

(2010) Katalin Csilléry et al.   TRENDS IN ECOLOGY & EVOLUTION

Recombination, Reservoirs, and the Modular Spike: Mechanisms of Coronavirus Cross-Species Transmission

(2009) R. L. Graham et al.   JOURNAL OF VIROLOGY

Non-linear regression models for Approximate Bayesian Computation

(2009) Michael G. B. Blum et al.   STATISTICS AND COMPUTING

A population genomic approach to map recent positive selection in model species

(2008) P. PAVLIDIS et al.   MOLECULAR ECOLOGY