Joe Root won't be a part of the game as he would be attending the birth of his child.
The first Test between England and West Indies is scheduled to start from July 8, followed by the next two matches of the series in Manchester.
The decision by the ECB of showing solidarity to the black community came after the West Indies side announced that they would be wearing 'Black Lives Matter' logos on their playing jerseys.
In the statement released by the England and Wales Cricket Board (ECB), it was informed that Sam was tested for novel coronavirus and he will not be a part of the practice match.
After missing the first Test, the England skipper is expected to join back the squad for the final two Tests.
West Indies are likely to wear the shirts with BLM logo for the first time in the four-day warm-up match to be played at the Old Trafford this week.
Assistant coaches Roddy Estwick and Rayon Griffith will oversee the team's second warm-up match, which begins on Monday, before both the sides battle it out in the first Test at Southampton.
England's Test series against West Indies will be the first international action for the fans to witness in the post-coronavirus world.
Root also said that he could miss the opening Test.
Virdi has played 23 first-class games for Surrey, picking 69 wickets.