Tapendra Ghai was placed second after a round of 1 over par.
Manu Gandas occupied the third position by finishing his second round at 1 over par.
On a day where the golf course restricted the players to a conservative play, Viraj managed to break the shackles by making birdies on the 2nd,4th and 6th holes before dropping a shot on the par 5 8th hole to take the turn at 2 - under par.
On the back nine Viraj faltered to drop two more shots and finish the day at level par.
"It was tough out there today; I had some great opportunities to score but could not make it count. I hope to play a better game of golf tomorrow and widen my lead here" said the 15 year-old- boy from Kolkata.
In Category B, Karandeep Kochar finished at 3 - over par to be tied on top of the leader board along with Kartik Sharma who carded a 4 - over par round on Wednesday. Adilbir Singh took the third position with the best round of the day in category B at 2 - over par.
Meanwhile, overnight leader Arjun Prasad slipped to the 4th position after carding an 11 - over par round on the second round.
Top scores after 36 holes
139 Viraj Madappa (67, 72); 144 Tapendra Ghai (71, 73); 147 Manu Gandas (74, 73); 148 Ritwik Jain (75, 73); 150 Yuvraj Sandhu (75, 75), Mohan Sardar (74, 76)
152 Karandeep Kochar (77, 75), Kartik Sharma (76, 76); 153 Adilbir Singh (79, 74); 156 Arjun Prasad (79, 74)
--IBNS (Posted on 16-10-2013)