Why are adenoviral vector vaccines safe in terms of insertion mutagenesis due to genome integration and E4 region's proteins effects?

Question

Disclaimer: I'm neither a genetics professional nor an anti-vax fanatic, I just tried to compare COVID-19 vaccine types currently available on the market and got some questions that I'd like to answer rationally.

Some of the vaccines that are being actively used now are based on adenoviral vectors, such as ChAdOx1, Ad26, or Ad5. These vectors are replication-defective, usually due to removed E1/E3 regions.

I looked for existing information about adenoviral vectors and found some facts that may relate to safety, but I can't conclude if they are rational or not for vaccine applications, since most studies are made for gene therapy or animal models.

Proteins activity

Wild-type adenoviruses are considered to be able to lead to tumors in rodents (Wiki: DNA oncoviruses), mostly due to E1 region activity, but E4 also adds to its oncogenic effect (Cell transformation by the adenovirus oncogenes E1 and E4), and may affect DSB repair (Expression of the adenovirus E4 34k oncoprotein inhibits repair of double-strand breaks). That may be related to the “hit-and-run” mutagenesis theory.

For Ad9, E4 alone can show that effect, E1 is dispensable (Adenovirus type 9 E4 open reading frame 1 encodes a transforming protein required for the production of mammary tumors in rats)

Genome integration

It's thought that adenoviruses do not integrate into the host genome, since they don't have a tool for that, but occasionally it happens with low probability (10^-3 .. 10^-7 per cell), particularly in cells where the virus can't replicate and lysis doesn't happen, which is always the case for replication-defective vectors (Chromosomal Integration of Adenoviral Vector DNA In Vivo, Frequency and Stability of Chromosomal Integration of Adenovirus Vectors, Insertion vectors for gene therapy, Illegitimate DNA integration in mammalian cells, Viral Vectors: The Road to Reducing Genotoxicity, Viral Epigenetics).

That raises questions about the possibility of insertional mutagenesis. As I see, such questions are often discussed in the context of DNA vaccines, but extremely rarely for adenoviral vectors which also deliver DNA into cells.

Finally, the question itself:

Should risks of insertional mutagenesis due to viral genome integration and E4 region's proteins activity be considered and discussed or they are not important / do not exists at all for adenoviral vector vaccines? Have I missed any studies about these topics?

Can these risks be estimated in numbers and compared with similar natural events?

Answer 1

This question envisages putative harmful changes arising in host tissue cells infected with the replication-defective virus of a 'vectored' vaccine.

The scenarios of the question leave out of account a significant factor that opposes such putative harms. That is, one of the main purposes and effects of such vectored virus vaccines, which is to produce an adaptive cytotoxic T-cell immune response, targeted on (cell-surface-displayable fragments of) the viral gene-products (i.e. proteins) foreign to the tissues of the vaccinated host.

The aim of stimulating cytotoxic T-cell responses from vaccination is especially important against pathogens such as viruses (or intracellular parasites such as malaria) that disappear into the interior of cells of the host, and thereby become 'invisible' to circulating antibodies of the host immune system. This makes the antibody part of the response less useful against such pathogens.

Once such cytotoxic T-cells have been developed, they circulate and can detect and kill host tissue cells displaying fragments of those 'foreign' proteins on which the T-cells are targeted.

All of the host tissue cells infected by the vaccine virus are in this targeted category, and the consequence is that those infected host tissue cells have only a short life. They also are generally somatic cells with little cell-division, e.g. where the vaccine is given intramuscularly. Also, the replication-defect of the vaccine virus means that the vaccine-virus-infected cells are number-limited by the number of infectious units in the vaccine dose, there is no production of fresh generations of virus particles.

These factors and the processes of the cytotoxic immune response altogether oppose any likelihood of the putative harms envisaged by the question. The cited prototypes of those harms appear not to be reported in respect of situations that arise after vaccination with vectored virus vaccines.

(Supporting background can be found described and explained in the various editions of Janeway's 'Immunobiology'. The original author died in 2003, but the later editions have been retitled "Janeway's Immunobiology", in memoriam, to mark his founding contributions, e.g. the 9th edition (2017) is from authors/editors K Murphy & C Weaver.)