A mutated virus for vaccine development must retain antigenicity in order to induce an immune response in the recipient. Reduced pathogenicity, altered host range, or altered target cell specificity would all be desired traits in a vaccine strain.

Viral RNA polymerases do not have the same proof-reading ability as DNA polymerases. This is a contributing factor to the difficulty of making vaccines from RNA viruses.  

Retroviruses do have a single-stranded RNA genome, but they use DNA intermediates in replication. Retroviruses utilize reverse transcriptase to convert viral RNA into complementary DNA, which is then copied to produce double-stranded viral DNA.

Recombination by independent assortment occurs in viruses that have segmented genomes. Genes are randomly assorted, which can result in the generation of viruses with new antigenic determinants (antigenic shift).

Reverse transcriptase is an enzyme that can transcribe DNA from RNA, and is used by retroviruses to make a DNA transcript of their own RNA genome. The DNA is then inserted directly into the host’s genome. Endocytosis and membrane fusion are different terms for the process by which viruses insert material into the host cell, but not directly into the genome. Retrotransposons are genetic elements in eukaryotic cells that use reverse transcriptase to duplicate themselves throughout the cell genome. Telomerase is a type of reverse transcriptase found in eukaryotic cells that adds repeated sequences to the ends of chromatids.

Viruses are not universally recognized as living organisms. One of many differences between viruses and other organisms is that all other living organisms contain both DNA and RNA, while viruses only contain one or the other. Some RNA viruses are able to produce DNA using mechanisms such as reverse transcription, but this does not happen until after the virus infects the host cell.

In a cell infected by more than one strain of virus, the segments of the different strains can be combined during viral assembly. Transduction is when DNA is introduced to a cell by a viral vector. Conjugation is when bacteria insert genes into other cells, usually other bacteria, using a pillus. Genetic drift is a term in evolution that applies to all organisms, where allele frequencies in a population change due to random chance. Antigenic drift is when viruses accumulate mutations over time.

Viruses have an enormous variety of genome structures, more than any phylum of organism. They have a variety of ways of expressing their genes and replicating, all involving using the host cell’s own machinery.

Viruses that have high-fidelity transcriptases have relatively low mutation rates. Conversely, viruses with low-fidelity transcriptases have relatively high mutation rates. Generally, the higher the fidelity of any enzyme involved in replication of viral nucleic acid, the lower the mutation rate. 

Spikes are either composed of hemagglutinin protein (HA) or protein neuraminidase (NA). HA helps the virus link with the host cell membrane while NA allows the release of a newly formed viral particle from the host cell.