The Green Flu is the name given to the zombie-esque virus found in Left 4 Dead to by the government organization CEDA. Although the virus itself seems to be a heavily mutated form of rabies ( transferred by bite) that causes the host body to change into a deranged and biologically unstable state, CEDA has chosen to give it the misleading "Flu" moniker which indicates ignorance of the virus by CEDA or active deception towards the public as to the virus's true nature.
The Green Flu appears to only be transferable through a bite or possibly direct contact with infected bodily fluids (Ex: Boomer Bile). It is possible that there could indeed be a Influenza type strain of the virus acting concurrently alongside the rabies strain (which would lend some credibility to CEDA's claims) though there is some contradicting evidence to debunk this theory, though it would explain the rapid pace the virus has spread at. There is also some evidence that points to a mutation of Mad Cow disease as piles of dead cows with scalped skulls, as part of CEDA's testing, in both games though this could have been due incompetence on CEDA's part.
On the other hand, there is an abundance of information to indicate that the virus is indeed a strain of rabies. Several bodies can be found throughout the Left 4 Dead games in which large chunks of flesh are missing on several dead bodies that seems to have possibly come from an Infected's bite. The Church Guy in the original Left 4 Dead sometimes mentions that he has been bitten prior to his transformation as well.
It is currently unknown how long it takes the Green Flu to fully take effect and turn the host into a fully infected zombie. Some claims found throughout the game range from days to several minutes, and as none of the Survivors are ever turned into Infected there is no way for the player to gauge or test this intermediary stage of the virus. It may be that as the infection exists and mutates for longer periods of time that the period between infection and full blown zombification may be significantly shortening.
What is peculiar about the Green Flu is that it is atypical in comparison to other zombie plagues in that the transformed hosts do not appear to be interested in spreading the disease; perhaps the sole exception of this being the Boomer, but as his bile serves to attract the horde the risk of infection may just be an unintended collateral effect. The Common Infected and several Special Infected attack only using their claws, never their teeth, and when a Survivor is slain they simply stand around their kill as if nothing had happened. This may be due to the fact that they can sense immunity tot he Green Flu in a victim by some means, and Church Guy's bite would validate such a hypothesis.
The Infected, or the victims who have succumb to Green Flu, are often considered zombies or to be more accurate members of the living dead. While the word "zombie" has come under some scrutiny lately we can be sure that Green Flu victims are definitely not reanimated, simply changed.
Biologically, we know quite a lot about Infected qualities. They have very good vision at all times of day and privy to the location of their fellow Infected and any Survivors by some unknown means. It is very possible that the Infected are able to accomplish this feat through an acute sense of smell as Boomer Bile has been proven to draw any and all Infected within an area to a given spot. Aside from that the Infected often have severely damaged and discolored flesh and glowing eyes which can be seen from several feet away in areas of moderate darkness.
Unlike a stereotypical zombie, the Infected do not pass away before undergoing their change. Although a change from human to Infected has never been visually observed in game, we do know from Church Guy that the change most likely takes place while the victim is fully conscious and that they simply reach a certain point where their will finally gives out and the change occurs.
From observing Infected behavior in game, we also know that the Infected are well aware of each other, unlike regular zombies, and often communicate with each other physically through acts of violence and more often vocally through shrieks and (as noted by some Survivor graffiti) perhaps even speech. This once again gives evidence to the theory that the Infected are not dead but have simply been altered by the Green Flu virus.
The goal of the Infected is not clear though as their motivations seems sporadic at best. As mentioned previously, the Infected do not seem very interested in spreading the virus as much as simply killing anyone who hasn't been turned into an Infected. It is very likely that the Infected indeed do not have any ultimate goal at all and that the Green Flu Infected are simply deranged humans slowly dying from a terrifying disease.
The Green Flu has the ability to mutate its victims into not just enraged hordes of Common Infected, but also powerful mutated Special Infected as well. Several of these include the Boomer, Smoker, and Hunter; each of which posses unique abilities completely independent of their fellow Special Infected or Common Infected.
The variation in the mutation may be due to the biological make-up of the host prior to infeciton as the clothes and habits of the Special Infected give us clues as to who they may have been prior to contracting Green Flu. For example, the Hunter is seen wearing an attire typical of a someone who practices parkour. This would tie in with his above average speed, lunging attacks, and his ability to jump off of walls.
However, the one aspect of Green Flu mutation that the Left 4 Dead franchise is somewhat unclear about is how the mutation occurs. In the opening scene of the original Left 4 Dead Bill states that the Infected have begun to change recently due to goo (most likely Boomer Bile) he finds on the ground. One could infer that this means the Infected themselves are being transformed, though this may not be the case. Once again, Church Guy serves as an excellent case study as he will always turn into a Special Infected upon transformation. This could mean that the virus itself is mutating as opposed to the Infected themselves and could lead to evidence in support of the two strain theory as an influenza strain could be creating Common Infected while bite victims of the rabies strain (like Church Guy) are transformed into Special Infected. A case against this could be made however due to the fact that the Left 4 Dead 2 Special Infected are far more mutated than their original incarnations.
Throughout both Left 4 Dead games it is stated several times that the Survivors are "immune" and thus it is impossible for them to turn into Infected. This could in fact be a false hope however as although they may be Immune to an airborne virus but, if the two strain theory is to be believed, none of the Survivors have been bitten so it is still a possibility that they could succumb to a rabies strain. This is unlikely however, as they are drenched in Infected blood and gore throughout the entirety of the game and have yet to show any signs of change.
However, despite being immune to the virus, there are several CEDA notices along with many Survivor scribblings warning about "Carriers", or people who are immune to the Green Flu but can still carry it in their system. This seems somewhat like a paranoid reaction or further deception on CDA part through because, as previously discussed, the Green Flu would either already be spreading through the air or could only be transferred through direct fluid to fluid contact, an unlikely occurrence to happen between Survivors. The idea of a carrier is also somewhat upset by the fact that there are no recorded events (in game or in Survivor scribblings) in which a Survivor was ignored by the Infected despite them possibly carrying the Green Flu in their bodies. This could be explained by the fact that the Infected truly don't act to spread the virus and kill immune Survivors, though the rapid spread of the virus contradicts the theory.
The military, once it took over most of CEDA's operations in Left 4 Dead 2, began to sort Survivors coming into safe zones in two different groups while some were one group was shipped out while the other stayed. This is further evidence to suggest the military's legitimate belief in a carrier threat as piles of uninfected dead bodies can be found, along with the fact that the military personnel contacted at the end of The Parish in Left 4 Dead 2 mentions the fact that the Survivors could be carriers and for the helicopter pilot to prepare for such an occurrence. This could prove that carriers do in fact exist, though once again this could be due to CEDA's inaccurate data or simply heavy mis-communication in the military due to Washington DC already having succumb to the Green Flu.