The passenger, Mohammad Shariq, the prime suspect in the case, and the autorickshaw driver Purushotham Poojary sustained injuries in the blast.
Arafath Ali, who is the main handler of Shariq, is also absconding and a lookout notice has been issued against him.
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The incident occurred on Thursday night at Nanthur in Mangaluru, when the duo were travelling in a bus from Karkala to Mangaluru.
The NIA, which has jointly been investigating the case with the state police will now register a fresh FIR before taking up the probe.
She said the NIA has been active in Mangaluru for the last three months.
The NIA was roped into the investigation from day one of the investigation because of the nature of the blast.
Taxi Coimbatore police are verifying claims made by a taxi driver that he saw a person resembling Mohammad Shariq, prime suspect in the Mangaluru blast, at the Isha Yoga Centre.
On November 19, Mohammed Shariq, who was at large, was travelling in an autorickshaw with a cooker which exploded in Mangaluru injuring him and the driver.
The investigation in the case largely rests on Shariq’s interrogation.
Shariq is one among the other youth who have either been arrested or under surveillance in terror-related cases post the protests against the CAA and NRC in December 2020.
With demand growing for an NIA office in Mangaluru, Karnataka Home Minister Araga Jnanendra said the State government has brought this to the notice of the Centre.
ATS also conducted a probe by coordinating with Mangaluru Police regarding the parcels received by Shariq from an e-commerce platform while he was staying in Aluva.
In Shariq’s case, he is being handled by Arafath Ali, Abdul Matheen Taha and Musabir Hussain.
Meanwhile, Dakshina Kannada Deputy Commissioner Ravi Kumar MR assured all possible support to Poojary’s family.
The evidence collected from Shariq’s room at Lokanayakanagar in Mysuru was wrapped in sealed covers and sent to Mangaluru.
ATS is coordinating with Mangaluru police to receive more information about Shariq’s stay in Aluva.
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While Shariq was the main accused, Maaz and Yaseen were the second and third accused respectively.
He said it was fortunate that a major mishap was averted, but pointed out thatthe coastal region was becoming a haven for terrorists and terror activities.