Farrell will miss training on Friday but the Rugby Football Union (RFU) said he may still be able to play the match. The 30-year-old is isolating and will take further tests on Friday.
On Thursday a member of England support staff tested positive but the RFU says “England are continuing preparations” for Saturday’s match at Twickenham.
A statement added that all other players and staff had received negative results after a further round of testing on Thursday. Farrell is due to start at fly-half, with Marcus Smith on the bench after he missed several training sessions this week with a minor leg injury.
With George Ford left out of the autumn squad, Henry Slade – who is down to start at 13 – or replacement George Furbank may have to offer back-up at 10.
The RFU expects to know more about whether Farrell can play on Friday afternoon.
England: Steward; Radwan, Slade, Tuilagi, May; Farrell (capt), Youngs; Genge, George, Sinckler, Itoje, Hill, Lawes, Underhill, Curry.
Replacements: Blamire, Marler, Stuart, Ewels, Dombrandt, Mitchell, Smith, Furbank.