Callum McManaman 'worldie' takes Wigan Athletic up to minus two points following Northampton Town victory
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Northampton came close to opening the scoring with only a minute gone, when hit Sam Tickle's left-hand post from inside the six-yard box off Patrick Brough's cross.
At the other end, Wigan were claiming a penalty when Charlie Wyke appeared to be pushed as he competed for a cross, but nothing was given.
The visitors were holding their own, though, and they deservedly took the lead with 24 minutes gone.
Matt Smith was penalised for a foul on Mitchell Pinnock, and Sam Hoskins curled a wonderful free-kick over the wall and into the top corner of the net.
Wigan's hopes of an immediate equaliser were thwarted when Stephen Humphrys and Matt Smith fired wide, with Charlie Wyke also heading just off target.
Shaun Maloney opted to make an early change only 10 minutes after the restart, with Callum McManaman taking over from Scott Smith, who had made an encouraging first league start.
And Latics immediately upped their game, with Sean Clare releasing Humphrys, whose shot was parried away to McManaman, whose cross back in was headed just wide by Callum Lang.
Marc Leonard went into the book for chopping down McManaman in full flow, with Cobblers boss Jon Brady also receiving a caution in the technical area.
Maloney changed it again with 20 minutes to go, sending on forward Chris Sze for centre-back Liam Morrison, with midfielder Matt Smith dropping back into a back three.
And the equaliser arrived within two minutes, with Charlie Hughes heading home a pinpoint Tom Pearce cross.
It was all Wigan at this point, and the winning goal duly arrived with 11 minutes to go.
Seconds after Brough had fired wide for Northampton, McManaman cut in off the left before curling a left-footed strike into the top corner from the edge of the box.
After a second member of the Cobblers management team, assistant manager Colin Calderwood, was yellow-carded, there was still time for Wyke to head against the post from all of a yard.
But Latics were able to negotiate the seven added minutes to record a second successive league victory.