Professor Hasnain has made outstanding contributions to molecular pathogenesis and in designing innovative pioneering approaches for intervention against human pathogens. Focusing on host pathogen interaction in baculovirus infected insect cells, he identified the seminal importance of host factors in regulating over expression of heterologous genes and highlighted the importance of baculovirus anti-apoptic p35 protein and its mechanism of action during viral pathogenesis.

Using a very disruptive innovation approach, he co-designed a synthetic vaccine candidate gene corresponding to the major B and T cell epitopes of Plasmodium falciparum malaria based on mapping of domains, conferring natural immunity in malaria endemic patients, which after successful in vitro studies is now under GMP scale manufacturing for clinical trial. He co-identified molecular determinants for HBV vaccine escapees and helped design effective alternative clinical treatment regimes. He and his colleagues established genotype phenotype correlation in Indian patients with primary congenital glaucoma and developed simple rapid genetic screens that were used successfully for intervention against blindness in hundreds of children.

His laboratory discovered geographic partitioning of M.tb. isolates and introduced the concept of ‘geographic genomics’, wherein, depending on the local niche, the pathogen evolves with a specific signature. Analyses of such signatures in the clinical isolates of M.tb. in India, using molecular epidemiological approaches revealed the presence of ancestral, ancient and less virulent isolates which explains the lack of correlation between infection rate and disease burden of TB in India. Based on extensive genetic mapping of clinical isolates he proposed rifampicin as a surrogate marker for MDR – a concept adopted almost universally – thereby negating the need to do multi drug testing to determine MDR. His discovery of important functions of the hypothetical PE/PPE proteins present exclusively in the genus Mycobacterium, in “immune quorum sensing”, molecular mimicry and hijack of the host machinery for pathogen survival and dissemination has lead to a paradigm shift in our understanding of molecular pathogenesis.