Discriminating self from non-self in nucleic acid sensing

M Schlee, G Hartmann - Nature Reviews Immunology, 2016 - nature.com
Innate immunity against pathogens relies on an array of immune receptors to detect
molecular patterns that are characteristic of the pathogens, including receptors that are …

Synonymous but not silent: the codon usage code for gene expression and protein folding

Y Liu, Q Yang, F Zhao - Annual review of biochemistry, 2021 - annualreviews.org
Codon usage bias, the preference for certain synonymous codons, is found in all genomes.
Although synonymous mutations were previously thought to be silent, a large body of …

Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense

X Xia - Molecular biology and evolution, 2020 - academic.oup.com
Wild mammalian species, including bats, constitute the natural reservoir of betacoronavirus
(including SARS, MERS, and the deadly SARS-CoV-2). Different hosts or host tissues …

SARS-CoV-2 is restricted by zinc finger antiviral protein despite preadaptation to the low-CpG environment in humans

R Nchioua, D Kmiec, JA Müller, C Conzelmann, R Groß… - MBio, 2020 - Am Soc Microbiol
Recent evidence shows that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-
2) is sensitive to interferons (IFNs). However, the most effective types of IFNs and the …

Theoretical basis for stabilizing messenger RNA through secondary structure design

HK Wayment-Steele, DS Kim, CA Choe… - Nucleic acids …, 2021 - academic.oup.com
RNA hydrolysis presents problems in manufacturing, long-term storage, world-wide delivery
and in vivo stability of messenger RNA (mRNA)-based vaccines and therapeutics. A largely …

Origins and challenges of viral dark matter

SR Krishnamurthy, D Wang - Virus research, 2017 - Elsevier
The accurate classification of viral dark matter–metagenomic sequences that originate from
viruses but do not align to any reference virus sequences–is one of the major obstacles in …

RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies

F Tulloch, NJ Atkinson, DJ Evans, MD Ryan… - elife, 2014 - elifesciences.org
Mutating RNA virus genomes to alter codon pair (CP) frequencies and reduce translation
efficiency has been advocated as a method to generate safe, attenuated virus vaccines …

KHNYN is essential for the zinc finger antiviral protein (ZAP) to restrict HIV-1 containing clustered CpG dinucleotides

M Ficarelli, H Wilson, R Pedro Galão, M Mazzon… - Elife, 2019 - elifesciences.org
CpG dinucleotides are suppressed in most vertebrate RNA viruses, including HIV-1, and
introducing CpGs into RNA virus genomes inhibits their replication. The zinc finger antiviral …

Development of a new oral poliovirus vaccine for the eradication end game using codon deoptimization

JL Konopka-Anstadt, R Campagnoli, A Vincent, J Shaw… - npj Vaccines, 2020 - nature.com
Enormous progress has been made in global efforts to eradicate poliovirus, using live-
attenuated Sabin oral poliovirus vaccine (OPV). However, as the incidence of disease due to …

The evolutionary pathway to virulence of an RNA virus

A Stern, M Te Yeh, T Zinger, M Smith, C Wright, G Ling… - Cell, 2017 - cell.com
Paralytic polio once afflicted almost half a million children each year. The attenuated oral
polio vaccine (OPV) has enabled world-wide vaccination efforts, which resulted in nearly …