Related Experiment Video

Updated: Aug 12, 2026

Prediction of HIV-1 Coreceptor Usage Tropism by Sequence Analysis using a Genotypic Approach

Prediction of HIV-1 Coreceptor Usage Tropism by Sequence Analysis using a Genotypic Approach

Published on: December 1, 2011

Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in

Haoyu Zhou^1,2, Ruohan Ren^1,3, Stephen Shing-Toung Yau^1,4

¹Yanqi Lake Beijing Institute of Mathematical Sciences and Applications (BIMSA), Beijing, China.

Frontiers in Cellular and Infection Microbiology

|February 10, 2023

Abstract:

Comprehensive identification of possible target cells for viruses is crucial for understanding the pathological mechanism of virosis. The susceptibility of cells to viruses depends on many factors. Besides the existence of receptors at the cell surface, effective expression of viral genes is also pivotal for viral infection. The regulation of viral gene expression is a multilevel process including transcription, translational initiation and translational elongation. At the translational elongation level, the translational efficiency of viral mRNAs mainly depends on the match between their codon composition and cellular translational machinery (usually referred to as codon adaptation). Thus, codon adaptation for viral ORFs in different cell types may be related to their susceptibility to viruses. In this study, we selected the codon adaptation index (CAI) which is a common codon adaptation-based indicator for assessing the translational efficiency at the translational elongation level to evaluate the susceptibility to two-pandemic viruses (HIV-1 and SARS-CoV-2) of different human cell types. Compared with previous studies that evaluated the infectivity of viruses based on codon adaptation, the main advantage of our study is that our analysis is refined to the cell-type level. At first, we verified the positive correlation between CAI and translational efficiency and strengthened the rationality of our research method. Then we calculated CAI for ORFs of two viruses in various human cell types. We found that compared to high-expression endogenous genes, the CAIs of viral ORFs are relatively low. This phenomenon implied that two kinds of viruses have not been well adapted to translational regulatory machinery in human cells. Also, we indicated that presumptive susceptibility to viruses according to CAI is usually consistent with the results of experimental research. However, there are still some exceptions. Finally, we found that two viruses have different effects on cellular translational mechanisms. HIV-1 decouples CAI and translational efficiency of endogenous genes in host cells and SARS-CoV-2 exhibits increased CAI for its ORFs in infected cells. Our results implied that at least in cases of HIV-1 and SARS-CoV-2, CAI can be regarded as an auxiliary index to assess cells' susceptibility to viruses but cannot be used as the only evidence to identify viral target cells.

Insights

This study used the codon adaptation index (CAI) to assess human cell susceptibility to HIV-1 and SARS-CoV-2. Viral CAI values were generally lower than endogenous genes, suggesting incomplete adaptation, but CAI can aid in predicting viral target cells.

Area of Science:

Virology
Molecular Biology
Bioinformatics

Background:

Viral susceptibility is determined by factors including cell surface receptors and efficient viral gene expression.
Translational efficiency, influenced by codon adaptation, is critical for viral gene expression and infection.
Codon Adaptation Index (CAI) measures translational efficiency at the elongation level.

Purpose of the Study:

To evaluate human cell susceptibility to HIV-1 and SARS-CoV-2 using CAI.
To refine viral infectivity analysis to the cell-type level.
To investigate the impact of viral infection on cellular translational mechanisms.

Main Methods:

Calculated CAI for viral open reading frames (ORFs) in various human cell types.
Correlated CAI with translational efficiency using endogenous genes as a benchmark.
Compared CAI-based susceptibility predictions with experimental findings.

Main Results:

Viral ORFs generally exhibited lower CAI values compared to highly expressed endogenous genes, indicating suboptimal adaptation to host translational machinery.
CAI-based susceptibility predictions largely aligned with experimental data, though exceptions were noted.
HIV-1 infection decoupled CAI and translational efficiency of endogenous genes, while SARS-CoV-2 increased viral ORF CAI in infected cells.

Conclusions:

CAI serves as a valuable auxiliary index for assessing cell susceptibility to viruses like HIV-1 and SARS-CoV-2.
CAI alone is insufficient for definitively identifying viral target cells.
Different viruses modulate host cellular translational mechanisms distinctively.

Read full analysis

Keywords:

HIV-1 SARS-CoV-2 codon adaptation index (CAI)target cells translational efficiency

More Related Videos

Pairwise Growth Competition Assay for Determining the Replication Fitness of Human Immunodeficiency Viruses

Pairwise Growth Competition Assay for Determining the Replication Fitness of Human Immunodeficiency Viruses

Published on: May 4, 2015

Single-cell Quantitation of mRNA and Surface Protein Expression in Simian Immunodeficiency Virus-infected CD4+ T Cells Isolated from Rhesus macaques

Single-cell Quantitation of mRNA and Surface Protein Expression in Simian Immunodeficiency Virus-infected CD4+ T Cells Isolated from Rhesus macaques

Published on: September 25, 2018

Related Concept Videos

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 for adaptive...

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 stands for...

Coronavirus

Coronavirus

Coronaviruses, including the severe acute respiratory syndrome coronavirus (SARS-CoV), are enveloped viruses characterized by their single-stranded, positive-sense RNA genome and helical nucleocapsid structure. The hallmark of these viruses is their club-shaped spike (S) glycoproteins that protrude from the viral envelope, facilitating attachment to host cells. Typically, coronaviruses infect the upper respiratory tract, often causing mild or asymptomatic disease. However, certain strains like...

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

Applications of self-assembled monolayers (SAMs) in perovskite tandem photovoltaics.

Chemical communications (Cambridge, England)·2026

A single-cell spatiotemporal manifold of tissue morphology and dynamics.

Cell reports methods·2026

A Biofabricated Human Acinus-on-a-Chip Unveils Mechanotransductive Drivers of Ventilator-Induced Lung Injury via Decoupling Volutrauma and Barotrauma.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026

Dual-Polysaccharide Reinforced Pickering Emulsion Gels for Tailoring Microstructure and Enhancing 3D Printing Performance.

Foods (Basel, Switzerland)·2026

Volatile aroma profiles and associated microbiota of Yunnan Shiping sour-pulp-fermented stinky tofu.

Food chemistry: X·2026

Functional data analysis of college students' sleep patterns and their relationships with academic performance and social networks: A four-year longitudinal study.

PloS one·2026

See all related articles