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Electronic digitization of biomolecules for rapid and real-time detection of human pathogens using nanopore technology

Introduction

The incidence of infectious and other tropical diseases has registered a geometric growth in last few decades in India. Such a growth pattern has brought India on a global map to represent one of the countries harboring highest number of infectious diseases including Tuberculosis, Dengue, Chikan Gunea and Malaria. As a result the Indian population also faces a serious threat of bacterial resistance due to frequent and non judicious use of broad spectrum antibiotics. It is indeed more dressing to note that in India there are about 2 to 2.5 million TB cases out of which 30% do not get access to adequate treatment. The situation is getting grimmer with the passage of time as the most affected population deprived of treatment comes from rural areas. The confluence of environmental conditions, socio-economic factors, lack of appropriate diagnostic facilities contributed to ever increasing burden of infectious diseases in India.

The emerging and re-emerging infectious diseases also include the diseases of zoonotic origin and there appears to be no effective control to prevent or contain the incidence of such diseases. The major handicap has been non availability of rapid, robust and real time detection techniques for identification of human pathogens with greater specificity and due to which a large number of patients either remain undetected/undiagnosed or do not receive evidence based and timely treatment. This project therefore envisages the use of biosensors ( nanopore) for rapid and real time detection of human pathogens viz viruses, bacteria, parasites etc. causing most of the currently prevalent zoonotic and non zoonotic diseases in the country.

PROPOSED METHODOLOGY

DNA is a Bio-molecule that encodes genetic instructions and is considered to be a bio print of human life. It can therefore be contemplated that DNA sequencing would have profound impact on a large number of human diseases. The biosensor or nanopore based detection of human pathogens through table top DNA sequencing and subsequent web based pipeline to be used for streaming of real time sequenced data to genomic data cloud and detect the presence of human pathogens like commonly prevalent viruses (Dengue, CHIKV, HCV, Malaria etc.) and bacteria including tubercular bacillus.

Biological Nanopore Sequencing

Nanopore as such is a very tiny hole within a natural protein molecule and is used as biosensor by maintaining a voltage across the pore and changes may be measured as the DNA or its fragments pass through the hole. Such changes can delineate a pattern to distinguish between the bases of DNA molecule i.e. G,A,T and C. These uniquely characteristic streams of electronic sensing data pertaining to DNA, RNA or other proteins can be considered as digital information which is transmitted online through a web based pipeline for instant and rapid detection of various pathogens present in a clinical sample

APPLICATIONS

  • Digitization of biological samples and data streaming to the data cloud for real time analysis and detection of the presence of viral or bacterial pathogens in quickest possible time duration of 2-4 hrs.
  • Effective Use in monitoring of therapy response.
  • The bio sensor platform can be used in rural clinics or peripheral primary health centres
  • Collection and storage of digital information of biomolecules in database for future surveillance, monitoring and medical research and sharing of information.
  • Reliable and precise diagnosis using using ultra long reads having 10000-1000000 bases might providing the best coverage and specificity (99%), requiring only 1ug of DNA or RNA input
  • Simultaneus predictability of antibiotic resistance