The 34-year-old Spanish World Cup winner completed a big-money move from Barcelona in May.
The ICC last week unveiled tougher sanctions for ball tampering and sledging in a bid to improve on-field behaviour in the sport.
Van Avermaet leads Thomas, in second, by 2min 22secs, with Alejandro Valverde now up to third at 3:10.
The US finished with a final tally of 219 points while Poland came second on 162.
The modified route to run between Astrakhan and Moscow from July 21 to 27.
The Canadian will next face 2016 Gstaad champion Victorija Golubic.