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Visakhapatnam: England struggle to 103-5 in reply to India's 455 in the second Test in Visakhapatnam on Friday.
Ashwin picked up two wickets while Shami and debutant Jayant Yadav picked up one each.
On a pitch showing low bounce and some turn, the tourists slumped to 103-5, still 352 behind.
Joe Root made 53, but Haseeb Hameed was the only member of the top five to reach double figures.
After having the better of the drawn first Test in Rajkot, this was a chastening experience for England and much more in keeping with what was expected at the beginning of the tour.
With the pitch only set to deteriorate further, England's best chance of getting something out of this match was to get up and around India's first-innings total. Instead, it will now take something remarkable to avoid going 1-0 down in the five-match series.
Earlier, all-rounder Ravichandran Ashwin struck a crucial half-century before England bowled out India for 455 in the afternoon session.
Ashwin's fighting 58 came after England spinner Moeen Ali checked the Indian charge with three wickets in the morning session including skipper Virat Kohli for 167.
Ashwin put on 64 runs for the eighth wicket with debutant Jayant Yadav, who scored 35, guiding India to a respectable first innings score on a pitch that is expected to offer turn as the match progresses.
India, who resumed the day on 317 for four, were reduced to 363 for seven before Ashwin countered the England bowling attack.
Ashwin and Jayant Yadav hit nine boundaries between them as number 10 batsman Umesh Yadav (13) also joined the late flurry with three fours.
England pace spearhead James Anderson and Ali claimed three wickets each.
Brief scores
India - 455 (Kohli 167, Pujara 119, Ashwin 58, Moeen 3-98, Anderson 3-62)
England- 103 for 5 (Root 53, Ashwin 2-20)
Status - England trail by 352 runs
