VirusRecom: an information-theory-based method for recombination detection of viral lineages and its application on SARS-CoV-2

mRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant

(2022) Wilfredo F. Garcia-Beltran et al.   CELL

Ongoing Recombination in SARS-CoV-2 Revealed through Genealogical Reconstruction

(2022) Anastasia Ignatieva et al.   MOLECULAR BIOLOGY AND EVOLUTION

Deltacron: the story of the variant that wasn’t

(2022) Freda Kreier   NATURE

Possible recombination between two variants of concern in a COVID-19 patient

(2022) Yaqing He et al.   Emerging Microbes & Infections

Emergence of Within-Host SARS-CoV-2 Recombinant Genome After Coinfection by Gamma and Delta Variants: A Case Report

(2022) Ronaldo da Silva Francisco Junior et al.   Frontiers in Public Health

XE, XD & XF: what to know about the Omicron hybrid variants

(2022) Greg Basky et al.   CANADIAN MEDICAL ASSOCIATION JOURNAL

Genomic and epidemiological report of the recombinant XJ lineage SARS-CoV-2 variant, detected in northern Finland, January 2022

(2022) Erika Lindh et al.   Eurosurveillance

Culture and identification of a “Deltamicron” SARS‐CoV‐2 in a three cases cluster in southern France

(2022) Philippe Colson et al.   JOURNAL OF MEDICAL VIROLOGY

Recombination between SARS-CoV-2 Omicron BA.1 and BA.2 variants identified in a traveller from Nepal at the airport quarantine facility in Japan

(2022) Tsuyoshi Sekizuka et al.   JOURNAL OF TRAVEL MEDICINE

Recombinant SARS-CoV-2 variants XD, XE, and XF: The emergence of recombinant variants requires an urgent call for research – Correspondence

(2022) Chiranjib Chakraborty et al.   International Journal of Surgery

A Bayesian approach to infer recombination patterns in coronaviruses

(2022) Nicola F. Müller et al.   Nature Communications

Evolutionary analysis and lineage designation of SARS-CoV-2 genomes

(2021) Xiaolu Tang et al.   Science Bulletin

KwARG: Parsimonious reconstruction of ancestral recombination graphs with recurrent mutation

(2021) Anastasia Ignatieva et al.   BIOINFORMATICS

Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic

(2021) Ben Jackson et al.   CELL

The biological and clinical significance of emerging SARS-CoV-2 variants

(2021) Kaiming Tao et al.   NATURE REVIEWS GENETICS

Rampant C→U Hypermutation in the Genomes of SARS-CoV-2 and Other Coronaviruses: Causes and Consequences for Their Short- and Long-Term Evolutionary Trajectories

(2020) P. Simmonds   mSphere

Characteristics of SARS-CoV-2 and COVID-19

(2020) Ben Hu et al.   NATURE REVIEWS MICROBIOLOGY

Temporal signal and the phylodynamic threshold of SARS-CoV-2

(2020) Sebastian Duchene et al.   Virus Evolution

BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission

(2020) Zhi-Jian Zhou et al.   Sustainable Cities and Society

RDP5: A computer program for analysing recombination in, and removing signals of recombination from, nucleotide sequence datasets

(2020) Darren P Martin et al.   Virus Evolution

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

Repair of DNA damage caused by cytosine deamination in mitochondrial DNA of forensic case samples

(2018) Erin M. Gorden et al.   Forensic Science International-Genetics

Improved Algorithmic Complexity for the 3SEQ Recombination Detection Algorithm

(2017) Ha Minh Lam et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus

(2017) Ben Hu et al.   PLoS Pathogens

Viral evolution: beyond drift and shift

(2015) Benjamin D Greenbaum et al.   CURRENT OPINION IN MICROBIOLOGY

Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia

(2015) J. S. M. Sabir et al.   SCIENCE

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen 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 and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor

(2013) Xing-Yi Ge et al.   NATURE

Discovery of functional genomic motifs in viruses with ViReMa–a Virus Recombination Mapper–for analysis of next-generation sequencing data

(2013) Andrew Routh et al.   NUCLEIC ACIDS RESEARCH

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Viral reassortment as an information exchange between viral segments

(2012) B. D. Greenbaum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RDP3: a flexible and fast computer program for analyzing recombination

(2010) D. P. Martin et al.   BIOINFORMATICS

Coalescent Simulation of Intracodon Recombination

(2009) M. Arenas et al.   GENETICS