Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Single Nucleotide Polymorphisms-SNPs

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

Size and Structure of Viral Genomes

Size and Structure of Viral Genomes

Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...

Viral Mutations

Viral Mutations

A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...

Viral Recombination

Viral Recombination

Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.

Viral Structure

Viral Structure

Viruses are extraordinarily diverse in shape and size, but they all have several structural features in common. All viruses have a core that contains a DNA- or RNA-based genome. The core is surrounded by a protective coat of proteins called the capsid. The capsid is composed of subunits called capsomeres. The capsid and genome-containing core are together known as the nucleocapsid.

Leaky Scanning

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Ongoing Hepatitis A Transmission in Campania: A One Health Sentinel Event at the Human-Seafood-Environment Interface.

Journal of medical virology·2026

Same author

Detection of and Early Genomic Insights into Chikungunya Virus, Bolivia, 2025.

Emerging infectious diseases·2026

Same author

Integrated Downstream Analysis and Epidemiological Modelling of Hantavirus Infection: From Host Transcriptomics to Transmission Dynamics.

Pathogens (Basel, Switzerland)·2026

Same author

Orthohantavirus Infection Mimicking Acute Viral Hepatitis: An Underrecognized Clinical Presentation.

Pathogens (Basel, Switzerland)·2026

Same author

How technologies are driving digital innovation in mosquito surveillance systems: a global scoping review over the past decade.

BMJ public health·2026

Same author

Enhanced virulence and neuroinvasion of contemporary <i>Oropouche</i> virus strains in the AG129 mouse model.

Frontiers in microbiology·2026

Search research articles

Related Experiment Video

Updated: Jul 25, 2025

Production of a SARS-CoV-2 Virus-Like-Particle System to Investigate Viral Life Cycles In Vitro

Production of a SARS-CoV-2 Virus-Like-Particle System to Investigate Viral Life Cycles In Vitro

Published on: June 6, 2025

SARS-CoV CH.1.1 Variant: Genomic and Structural Insight.

Liliana Bazzani¹, Elena Imperia^2,3, Fabio Scarpa⁴

¹Sciences and Technologies for Sustainable Development and One Health, University Campus Bio-Medico of Rome, 00128 Rome, Italy.

Infectious Disease Reports

|June 27, 2023

Summary

A new COVID-19 variant, Omicron CH.1.1 "Orthrus," shows concerning mutations like L452R. Early analysis suggests potential for increased severity and transmission, requiring enhanced global surveillance.

Keywords:

CH.1.1 variant SARS-CoV-2 genomic surveillance mutational pattern profile

More Related Videos

Engineering Antiviral Agents via Surface Plasmon Resonance

Engineering Antiviral Agents via Surface Plasmon Resonance

Published on: June 14, 2022

Visualization of SARS-CoV-2 using Immuno RNA-Fluorescence In Situ Hybridization

Visualization of SARS-CoV-2 using Immuno RNA-Fluorescence In Situ Hybridization

Published on: December 23, 2020

Related Experiment Videos

Last Updated: Jul 25, 2025

Production of a SARS-CoV-2 Virus-Like-Particle System to Investigate Viral Life Cycles In Vitro

Production of a SARS-CoV-2 Virus-Like-Particle System to Investigate Viral Life Cycles In Vitro

Published on: June 6, 2025

Engineering Antiviral Agents via Surface Plasmon Resonance

Engineering Antiviral Agents via Surface Plasmon Resonance

Published on: June 14, 2022

Visualization of SARS-CoV-2 using Immuno RNA-Fluorescence In Situ Hybridization

Visualization of SARS-CoV-2 using Immuno RNA-Fluorescence In Situ Hybridization

Published on: December 23, 2020

Area of Science:

Virology and Molecular Epidemiology
Genomic Surveillance of Emerging Pathogens

Background:

The Omicron subvariant XBB.1.5 (
Kraken
) dominated global COVID-19 cases in early 2023.
A novel Omicron subvariant, CH.1.1 (
Orthrus
), emerged with the L452R mutation, previously seen in Delta and BA.4/BA.5 variants.

Purpose of the Study:

To preliminarily understand the global distribution of the emerging SARS-CoV-2 CH.1.1 variant.
To analyze the potential functional significance of CH.1.1 mutations regarding disease severity, vaccine resistance, and transmission.
To investigate the phylogenetic origins and circulation patterns of the CH.1.1 variant.

Main Methods:

Genomic data analysis combined with structural molecular modeling.
Homology modeling to assess interactions with ACE2 and electrostatic potential.
Phylogenetic analysis to determine evolutionary relationships and cryptic circulation.

Main Results:

The CH.1.1 variant shares approximately 73% of mutations with other Omicron strains.
Homology modeling suggests CH.1.1 may exhibit weakened ACE2 interaction and a more positive electrostatic potential surface compared to ancestral strains.
Phylogenetic analysis indicates CH.1.1 was circulating cryptically in Europe before its official detection.

Conclusions:

The CH.1.1 variant possesses mutations that warrant active surveillance due to potential implications for disease severity, vaccine efficacy, and transmissibility.
Genomic and structural analyses provide insights into the potential biological behavior of this emerging SARS-CoV-2 variant.
Whole genome sequencing is crucial for the effective detection and control of emerging viral strains like CH.1.1.