System.Data.SQLite

Also we found out that, the critical change in 1.0.100.00  which is the update of  Sqlite core library to the 3.12.1. As explained in the below link, the default page size has been changed to 4096 bytes and the default cache size is set to -2000 (which is 2000 KB). 

https://www.sqlite.org/pgszchng2016.html 

When we set the cache size to higher value (-100000) in the query string, the queries ran without any slowdown. Is this is an expected concequense of the update 3.12.1.