In human gene therapy, a genetically modified virus (a.k.a. a viral vector) can alter the genetic variation of a cell, but not all viral vectors do.
The process often begins with the delivery of or creation of a segment of viral double stranded DNA (containing the gene you want to introduce). Then typically an enzyme known as an integrase cuts the ends of the segment of viral DNA and also cuts open the cell's DNA. Then the viral DNA is integrated/ inserted into the cell's DNA. The connecting ends are ligated together and adjusted so that the nucleotide base pairs match up.
This in the future may affect the gene pool for instance if the viral DNA (your gene) was inserted in the middle of another gene or important regulatory sequence of the cell DNA, and this alteration may be passed on into offspring and become present in the gene pool, which could have bad effects.
The effects on the gene pool really depends on what the virus ends up doing. For example, it may fix the function of a damaged gene which is the goal, and allow for a working gene to be in the gene pool, which would be good. The problem with gene therapy is that it's difficult to predict 100% what the virus will do every time it is given to a patient.
But it's very important to consider that it will only affect the gene pool if the virus is able to enter and alter germ cells (reproductive cells). If the virus, enters somatic cells (regular body cells) this will not be passed on to future generations. So viruses can be designed to avoid germ cells and avoid this gene pool issue. Also, some viral vectors use viruses that do not integrate their DNA, the cells just express the viral DNA (create the desired protein from it) and over time the viral DNA is degraded/ lost which wouldn't pose this threat.
This is long, but I hope it helped!
