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There is no best combination, it must more likely be coherent with what you will do after.
In single player, you can take genes to prevent the price to increase in either transmission, symptoms or abilities. So it's wise to place it in the category that you will use more. By default, transmissions.
I think there is one for using active abilities as well, maybe a good idea when you will have to use them much, like for simian flu or necroa virus in mega brutal level.
Extremophile is interesting because even if the bonuses are probably very little, you have no penalty to consider on the other hand. And as your build must be written around your penalties and not your bonuses, it avoids you to have to consider the environment gene in your build.
Aquacyte is interesting because the main difficulty is usually islands, and every islands have an harbor.
The gene to get more DNA from red bubbles is interesting, as you know that in each game, you are sure to get a determinated number of red bubbles. It also helps you to become adapted faster when you enter in many various sorts of countries.
In coop, the question is easy to answer when you play support. The best genes are urbophobe, thermophobe, xerophobe. Start in Turkey, and take either no symptoms (slow infection) or cough and sneeze (fast infection) ; the killer has the skin way free for him.
In coop as killer, it really depends on your project. You have to know that if you create a double penalty (like starting in an urban country with rurophobe), you will need the level 2 to start to exist in the opposite characteristic. And then it's more efficient in your build to take the 2 levels in row.
But anyway, NEVER take base hydration, benign infection, deadly disinfectant, or unstable inception (if you are the killer).
In VS as well, it really depends on the strategy you project.
ATP Boost, will yield less DNA than alternatives but DNA at the start is much more valuable
Darwinist or Genetic Mimic, alternatives are generally detrimental
Aquacyte, spreading to islands is critical
Teracyte, for plagues that have forced infection mechanics like Fungus
Sympto-Stasis, by far the best gene in the game and critical to almost every build
Patho-Stasis, for Fungus and Bio-Weapon
For Necroa Virus
Spliced Activation, alternatives are generally useless
For Simian Flu
Latent Catalyst, Cortisol Sensitivity is generally useless and other alternatives are generally detrimental
Anything but Adrenal Surge or Viral Affinity, generally detrimental or useless in that order
For Shadow Plague
Healthy Eater, higher health pool means stronger Templar killing power
Budget Bat, critical to most speed run builds
Witch Doctor, higher health regen means stronger Templar killing power
For multiplayer, co-op and/or versus
Genes are generally used to accelerate the first few countries you plan to infect which matters more in versus since you basically can't infect every country against a good opponent