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Training Years: 2016-2017

Training Site: Byramjee Jeejeebhoy Medical College, Pune (BJMC)

Country: India

Mentor: Vidya Mave, MD; Amita Gupta, MD

Title: Use of MinION nanopore, a third-generation sequencing technology, to diagnose arboviruses in HIV +/- patients in India

Project Objectives:  Third generation sequencing with MinION nanopore is an emerging NGS technology, but has only been successfully demonstrated on a small number of laboratory specimens and limited clinical specimens. The successful development of a MinION nanopore platform to diagnose arboviruses would pave the way for the development of nanopore to diagnose other pathogens. By changing the menu of broad-based primers at the outset, the MinION platform could be expanded to test for other vector-borne and environmental pathogens of interest to low and middle income countries, including rickettsioses, leptospirosis, and Q fever

Aim 1: To assess the ability of using a two-tiered sequencing approach to diagnose arboviruses in clinical specimens: i) arbovirus-specific amplification using broad-based multiplex primers and ii) 3rd generation nanopore sequencing;

Aim 2: To characterize the epidemiology of arboviruses among patients presenting with acute febrile illness in Pune, India.

Aim 3: We aim to assess the impact of HIV infection on the sensitivity of serological tests for arboviruses.

Aim 4: We aim to assess the impact of arboviral infection on the natural history of HIV infection.

NIH Support:  Fogarty fellowship postdoctoral training award

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