Nel returns after breaking his arm while Swinson is over a hand problem but Gray, struggling with a calf injury, and centre Duncan Taylor, who has a head injury, are yet to recover.
Scotland were hoping Gray, who missed Scotland's opening two Six Nations games, might add experience against England but the former British & Irish Lion's return has been delayed again.
There is a first call-up for uncapped 23-year-old Malcolm, but Townsend released Magnus Bradbury, Nathan Fowles, Murray McCallum and D'Arcy Rae back to their clubs.
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Scotland are looking for Calcutta Cup success for the first time in 10 years, having last won at Murrayfield by 15-9 in 2008. The Scots started this Six Nations campaign with defeat at Wales but bounced back to beat France in their second game.
Squad:
Backs: Mark Bennett (Edinburgh), Nick Grigg (Glasgow Warriors), Chris Harris (Newcastle Falcons), Stuart Hogg, Pete Horne, Ruaridh Jackson, Huw Jones (all Glasgow Warriors), Blair Kinghorn (Edinburgh), Greig Laidlaw (Clermont Auvergne), Sean Maitland (Saracens), Ali Price, Henry Pyrgos, Finn Russell, Tommy Seymour (all Glasgow Warriors), Matt Scott (Gloucester), Tim Visser (Harlequins)
Forwards: John Barclay (Scarlets), Simon Berghan (Edinburgh), Jamie Bhatti (Glasgow Warriors), David Denton (Worcester Warriors), Cornell du Preez, Grant Gilchrist (both Edinburgh), Jonny Gray (Glasgow Warriors), Luke Hamilton (Leicester Tigers), Rob Harley (Glasgow Warriors), Scott Lawson (Newcastle Falcons), James Malcolm (Glasgow Warriors), Stuart McInally, WP Nel (both Edinburgh), Gordon Reid (London Irish), Josh Strauss (Sale Sharks), Tim Swinson (Glasgow Warriors), Ben Toolis, Hamish Watson (both Edinburgh), Jon Welsh (Newcastle Falcons), Ryan Wilson (Glasgow Warriors)
(Reporting by Mark Gleeson; editing by Ken Ferris)
