Study explores role of APOBEC-mediated RNA editing in SARS-CoV-2 fitness

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped coronavirus with a single-stranded RNA genome. The SARS-CoV-2 exhibits moderate genetic variability, owing to the built-in auto-correct mechanism in their RNA-dependent RNA-polymerase (RdRP), which reverses errors during replication and transcription.

The two main sources of SARS-CoV-2 viral mutations are spontaneous random errors that remain unaffected by the proofreading mechanism of the RdRP and mutations of the viral genome that are mediated by host factors.

Background

Recent evidence suggests higher frequencies of mutational patterns with specific signatures as opposed to random genetic variations. These findings indicate that mutations induced by host factors are crucial in shaping the viral RNA mutational output. Meanwhile, the evolution mutations determine the viral genomic RNA outcome and evolution.

The APOBEC proteins belong to a family of cytosine deaminases; these deaminate cytosine to uracil (Cto-U) and engage in a variety of biological processes, for instance – innate and adaptive immunity against viral pathogens.

The APOBEC3 subfamilies A3A to A3H, impede DNA and RNA viruses. The SARS-CoV-2 mutational variants show a very high Cto-U mutation rate – which is likely due to RNA editing by host APOBECs.

The study

A new study posted on the Research Square* preprint server investigated whether APOBEC proteins can directly edit the RNA sequence of SARS-CoV-2 to generate C-to-U mutations. Here, the effects of such mutations on viral replication and viral progeny production were also assessed in an experimental system.

This article is the first in reporting experimental evidence of SARS-CoV-2 RNA edits by APOBEC3A, APOBEC1, and APOBEC3G—to produce C-to-U mutations.

Widespread vaccination and antiviral drug use have imposed additional selection pressure on the newer mutants of SARS-CoV-2, and thus, drug resistance and immune-escape mechanisms are likely to develop in the upcoming variants. The results of this study described that APOBEC enzymes – A1+A1CF, A3A, and A3G, can edit specific SARS-CoV-2 RNAs and may lead to mutations that enhance viral replication and fitness.

Findings

In this study, C-to-U editing on selected SARS-CoV-2 RNA segments by A1+A1CF, A3A, and A3G was examined through an APOBEC-RNA editing assay.

The three tested APOBECs showed varied editing rates at different RNA sites on the selected RNA transcripts. The findings specified that A1 plus and A1CF could effectively edit the AC motifs series of the viral RNA.

C in AC motif demonstrated a high mutation rate in SARS-CoV-2 and Rubella Virus. While A3A exhibited a dinucleotide UC motif. However, additional RNA structures around the UC and AC motifs must be crucial to ascertaining efficient editing of the UC or AC sites.

It was found that certain RNA targets with stem-loop structures were preferred for editing by the A3A and A1. Additionally, A3A and A1+A1CF are expressed in the human cells and organs infected by SARS-CoV-2, but not A3G. Hence, the practical application of A3A and A1+A1CF for editing the viral RNA genome is feasible.

A3A expression is stimulated by SARS-CoV-2 infection, which occurs in the lung epithelial cells. On the other hand, A1 (including cofactors – A1CF and RBM47) is expressed in the lower gastrointestinal tract or liver. SARS-CoV-2 variants showed higher AC motif mutations than those in the UC motif.

Numerous AC-to-AU mutations of the SARS-CoV-2 can be initiated by A1+A1CF-mediated editing in the infected host cells.

AC-to-AU editing necessitates the cofactor A1CF. Both cofactors of A1 have demonstrated interactions with the viral RNA. Therefore, these cofactors can employ A1 to target the viral RNA in the infected host cells.

This experiment also analyzed the influence of the three APOBECs on viral replication and progeny production. The findings showed that the deaminase activity of A3A enhances the proviral effect besides the supposed deamination-independent impact.

Although a majority of the C-to-U mutations detected will be probably lost, a few that enhance the survival of the virus will be selected and generate newer strains. It can be hypothesized that SARS-CoV-2 may evolve through the APOBEC mutational defense.

SARS-CoV-2 was shown to utilize A3A-mediated mutations for its benefit. It is observed that since the year 2020, a majority of mutations at UC241 (among the C-to-U mutations) were selected for better viral fitness. The UC241 to UU241 mutation probably endows the virus with better fitness.

Furthermore, editing of the host RNA or DNA by WT A3A possibly increases the viral RNA replication and viral progeny production.

Tremendous selection pressure is imposed on the virus due to its continued circulation amongst unvaccinated and vaccinated individuals and antiviral drug use. Thus, the results can help in predicting the newer variants of concern and the emergence of drug-resistant mutants.

*Important notice

Research Square publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Written by

Nidhi Saha

I am a medical content writer and editor. My interests lie in public health awareness and medical communication. I have worked as a clinical dentist and as a consultant research writer in an Indian medical publishing house. It is my constant endeavor is to update knowledge on newer treatment modalities relating to various medical fields. I have also aided in proofreading and publication of manuscripts in accredited medical journals. I like to sketch, read and listen to music in my leisure time.