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Steve Smith, who had a good hit on Wednesday evening, has also recovered from the wrist niggle.
The all-rounder will travel with the Aussie squad to India.
The 2018 outbreak killed 17 of the 18 persons who were confirmed to have been infected by the viral disease in Kozhikode.
Boult, Williamson, Neesham, fast bowler Tim Southee and wicketkeeper-batsman Tom Latham form a strong core of World Cup veterans but the squad also includes six players looking to make their debut at the 50-over tournament.
Fast bowling captain Pat Cummins, batsman Steve Smith, left-arm pacer Mitchell Starc and all-rounder Glenn Maxwell were all included despite still recovering from injuries.
Smith is nursing a tendon injury to his left wrist which will keep him sidelined for up to another four weeks. The report added that Starc is experiencing 'groin soreness'.
McGrath currently supervising a fast bowlers' camp organized by MRF Pace Foundation and Kerala Cricket Association at the Sports.
The three-day camp, organised by the MRF Pace Foundation and Kerala Cricket Association., began at the Sports Hub, Karyavattom, on Thursday morning.
Lyon, who is playing in his 100th consecutive Test, was running in to take a catch of Ben Duckett off the bowling of Cameron Green in the leg-side after tea, when he pulled up sharply while running towards the ball.
In reply to Australia's 416, England made 278/4 on the second day of the Ashes Test at Lord's.