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References from Balancing Genome Plasticity and Evolutionary Constraint During the Long-Term Evolution of Feline Coronaviruses. Local targets link to admitted publications; unresolved targets remain external evidence.
Signatures of omicron-like adaptation in early SARS-CoV-2 variants and chronic infection
10.1016/j.celrep.2025.116135 · 2025 · External reference
The coronavirus recombination pathway
10.1016/j.chom.2023.05.003 · 2023 · External reference
Origin and evolution of pathogenic coronaviruses
10.1038/s41579-018-0118-9 · 2019 · External reference
Recombinant canine coronaviruses related to transmissible gastroenteritis virus of Swine are circulating in dogs
10.1128/jvi.01937-08 · 2009 · External reference
Bovine-like coronaviruses in domestic and wild ruminants
10.1017/s1466252318000117 · 2018 · External reference
Feline Coronaviruses: Pathogenesis of Feline Infectious Peritonitis
10.1016/bs.aivir.2016.08.002 · 2016 · External reference
Feline infectious peritonitis epizootic caused by a recombinant coronavirus
10.1038/s41586-025-09340-0 · 2025 · External reference
10.3390/v12010083
10.3390/v12010083 · External reference
Differences in virus receptor for type I and type II feline infectious peritonitis virus
10.1007/s007050050336 · 1998 · External reference
Mutational analysis of aminopeptidase N, a receptor for several group 1 coronaviruses, identifies key determinants of viral host range
10.1128/jvi.01510-06 · 2007 · External reference
Characterization of CCoV-HuPn-2018 spike protein-mediated viral entry
10.1128/jvi.00601-23 · 2023 · External reference
An updated review of feline coronavirus: Mind the two biotypes
10.1016/j.virusres.2023.199059 · 2023 · External reference
Viral evolution: Animal viruses in pieces
10.1038/nrmicro.2016.133 · 2016 · External reference
The logic of virus evolution
10.1016/j.chom.2022.06.008 · 2022 · External reference
10.3389/fmicb.2022.850516
10.3389/fmicb.2022.850516 · External reference
MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
10.1093/molbev/mst010 · 2013 · External reference
trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses
10.1093/bioinformatics/btp348 · 2009 · External reference
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
10.1093/molbev/msaa015 · 2020 · External reference
SimPlot++: A Python application for representing sequence similarity and detecting recombination
10.1093/bioinformatics/btac287 · 2022 · External reference
RDP5: A computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets
10.1093/ve/veaa087 · 2021 · External reference
The SplitsTree App: Interactive analysis and visualization using phylogenetic trees and networks
10.1038/s41592-024-02406-3 · 2024 · External reference
DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets
10.1093/molbev/msx248 · 2017 · External reference
FUBAR: A fast, unconstrained bayesian approximation for inferring selection
10.1093/molbev/mst030 · 2013 · External reference
10.1186/s12917-025-04873-y
10.1186/s12917-025-04873-y · External reference
Intraspecific gene genealogies: Trees grafting into networks
10.1016/s0169-5347(00)02026-7 · 2001 · External reference
Continuous and Discontinuous RNA Synthesis in Coronaviruses
10.1146/annurev-virology-100114-055218 · 2015 · External reference
Genetic Variation and Evolution of the 2019 Novel Coronavirus
10.1159/000513530 · 2021 · External reference
10.1371/journal.pone.0106534
10.1371/journal.pone.0106534 · External reference
Recombination across distant coronavirid species and genera is a rare event with distinct genomic features
10.1128/jvi.01100-24 · 2024 · External reference
10.3390/v13071270
10.3390/v13071270 · External reference
The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes
10.1093/molbev/msab292 · 2022 · External reference
Host-Virus Arms Races Drive Elevated Adaptive Evolution in Viral Receptors
10.1128/jvi.00684-20 · 2020 · External reference
Nsp3 of coronaviruses: Structures and functions of a large multi-domain protein
10.1016/j.antiviral.2017.11.001 · 2018 · External reference
Adaptive Evolution of Feline Coronavirus Genes Based on Selection Analysis
10.1155/2020/9089768 · 2020 · External reference
10.1371/journal.pbio.3003471
10.1371/journal.pbio.3003471 · External reference
Host ZAP activity correlates with the levels of CpG suppression in primate lentiviruses
10.1073/pnas.2419489122 · 2025 · External reference
Elevation of CpG frequencies in influenza A genome attenuates pathogenicity but enhances host response to infection
10.7554/elife.12735 · 2016 · External reference
10.1371/journal.ppat.1011357
10.1371/journal.ppat.1011357 · External reference
Differences in virus receptor for type I and type II feline infectious peritonitis virus
10.1007/s007050050336 · ExternalCitation · doi-reference
Feline Coronaviruses: Pathogenesis of Feline Infectious Peritonitis
10.1016/bs.aivir.2016.08.002 · ExternalCitation · doi-reference
Nsp3 of coronaviruses: Structures and functions of a large multi-domain protein
10.1016/j.antiviral.2017.11.001 · ExternalCitation · doi-reference
Signatures of omicron-like adaptation in early SARS-CoV-2 variants and chronic infection
10.1016/j.celrep.2025.116135 · ExternalCitation · doi-reference
The logic of virus evolution
10.1016/j.chom.2022.06.008 · ExternalCitation · doi-reference
The coronavirus recombination pathway
10.1016/j.chom.2023.05.003 · ExternalCitation · doi-reference
An updated review of feline coronavirus: Mind the two biotypes
10.1016/j.virusres.2023.199059 · ExternalCitation · doi-reference
Intraspecific gene genealogies: Trees grafting into networks
10.1016/s0169-5347(00)02026-7 · ExternalCitation · doi-reference
Bovine-like coronaviruses in domestic and wild ruminants
10.1017/s1466252318000117 · ExternalCitation · doi-reference
Viral evolution: Animal viruses in pieces
10.1038/nrmicro.2016.133 · ExternalCitation · doi-reference
Origin and evolution of pathogenic coronaviruses
10.1038/s41579-018-0118-9 · ExternalCitation · doi-reference
Feline infectious peritonitis epizootic caused by a recombinant coronavirus
10.1038/s41586-025-09340-0 · ExternalCitation · doi-reference
The SplitsTree App: Interactive analysis and visualization using phylogenetic trees and networks
10.1038/s41592-024-02406-3 · ExternalCitation · doi-reference
Host ZAP activity correlates with the levels of CpG suppression in primate lentiviruses
10.1073/pnas.2419489122 · ExternalCitation · doi-reference
SimPlot++: A Python application for representing sequence similarity and detecting recombination
10.1093/bioinformatics/btac287 · ExternalCitation · doi-reference
trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses
10.1093/bioinformatics/btp348 · ExternalCitation · doi-reference
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
10.1093/molbev/msaa015 · ExternalCitation · doi-reference
The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes
10.1093/molbev/msab292 · ExternalCitation · doi-reference
MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
10.1093/molbev/mst010 · ExternalCitation · doi-reference
FUBAR: A fast, unconstrained bayesian approximation for inferring selection
10.1093/molbev/mst030 · ExternalCitation · doi-reference
DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets
10.1093/molbev/msx248 · ExternalCitation · doi-reference
RDP5: A computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets
10.1093/ve/veaa087 · ExternalCitation · doi-reference
Characterization of CCoV-HuPn-2018 spike protein-mediated viral entry
10.1128/jvi.00601-23 · ExternalCitation · doi-reference
Host-Virus Arms Races Drive Elevated Adaptive Evolution in Viral Receptors
10.1128/jvi.00684-20 · ExternalCitation · doi-reference
Recombination across distant coronavirid species and genera is a rare event with distinct genomic features
10.1128/jvi.01100-24 · ExternalCitation · doi-reference
Mutational analysis of aminopeptidase N, a receptor for several group 1 coronaviruses, identifies key determinants of viral host range
10.1128/jvi.01510-06 · ExternalCitation · doi-reference
Recombinant canine coronaviruses related to transmissible gastroenteritis virus of Swine are circulating in dogs
10.1128/jvi.01937-08 · ExternalCitation · doi-reference
Continuous and Discontinuous RNA Synthesis in Coronaviruses
10.1146/annurev-virology-100114-055218 · ExternalCitation · doi-reference
Adaptive Evolution of Feline Coronavirus Genes Based on Selection Analysis
10.1155/2020/9089768 · ExternalCitation · doi-reference
Genetic Variation and Evolution of the 2019 Novel Coronavirus
10.1159/000513530 · ExternalCitation · doi-reference
10.1186/s12917-025-04873-y
10.1186/s12917-025-04873-y · ExternalCitation · doi-reference
10.1371/journal.pbio.3003471
10.1371/journal.pbio.3003471 · ExternalCitation · doi-reference
10.1371/journal.pone.0106534
10.1371/journal.pone.0106534 · ExternalCitation · doi-reference
10.1371/journal.ppat.1011357
10.1371/journal.ppat.1011357 · ExternalCitation · doi-reference
10.3389/fmicb.2022.850516
10.3389/fmicb.2022.850516 · ExternalCitation · doi-reference
10.3390/v12010083
10.3390/v12010083 · ExternalCitation · doi-reference
10.3390/v13071270
10.3390/v13071270 · ExternalCitation · doi-reference
Elevation of CpG frequencies in influenza A genome attenuates pathogenicity but enhances host response to infection
10.7554/elife.12735 · ExternalCitation · doi-reference
