The ongoing global pandemic of SARS-CoV-2 (Covid-19) poses unique diagnostic and clinical management challenges in regions where seasonal epidemic-prone diseases are endemic. Diseases such as dengue, malaria, seasonal influenza, leptospirosis, chikungunya, scrub typhus and bacterial infections often present with febrile syndromes that mimic or co-exist with SARS-CoV-2 infection, complicating diagnosis and treatment. This document provides guidelines for preventing, diagnosing and managing such co-infections. A high level of suspicion is essential during the monsoon and post-monsoon seasons, taking into account region-specific disease prevalence. While the WHO's case definition for SARS-CoV-2 is broad and sensitive, the need for parallel testing for co-infections, in accordance with the protocols of the MoHFW, ICMR, NVBDCP and NCDC, is necessitated by overlapping clinical features. Ensuring the availability of reliable rapid diagnostic kits and applying integrated clinical and laboratory approaches are crucial to improving patient outcomes in the context of concurrent infections. Accessed on 26/08/2025.