Coming from anywhere outside of the US, you face VERY stiff competition, so anything less than top grades unfortunately does puts you at a disadvantage, I'm afraid. You will need to take the GRE and subject test(s) and achieve sparkling results to get noticed. Make sure you fully understand what you are applying for - most US PhD programmes dont really begin until after a year of selection - you enter a large yeargroup, take lectures, seminars, lab rotations and grueling exams before the final few a picked to go on to the PhD proper...