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HOD:
Dr. Luke Elizabeth Hanna
Scientist 'F'
Email: lukeelizebath.hanna@icmr.gov.in

Department of Virology & Biotechnology has been in the forefront providing high quality diagnostic and research support for various TB, HIV and HIV/TB clinical trials and research projects conducted by the National Institute for Research in Tuberculosis (NIRT). The laboratory has been accredited by International Agencies like the NIH and WHO, and has been participating successfully for many years in External Quality Assurance programs such as ISHTM-AIIMS EQAP for CBC, National EQAS for CD4 count and HIV serology, CDC proficiency testing program for total Nucleic Acid (tNA)-PCR for early infant diagnosis of HIV infection, NARI- EQAS Viral Load Proficiency Testing (VLPT) for HIV-1 viral load assay and NIH/WHO- VQA genotypic HIV drug resistance program. The focus of research in the laboratory include immune modulations and responses to tuberculosis infection, pathogenesis of HIV/TB co-infection, molecular characterization of HIV-1 subtype C strains circulating in the local population, and identification of novel compounds with anti-HIV activity. The workload of the department is managed by a professional team of 4 scientists, 10 technical officers, 6 technicians and 1 support staff who have permanent tenure and 2 technical officers, 3 technical assistants, 7 technicians, 1 date entry operator and support staff who work in various projects in the department in fixed tenure. At present, there are five research scholars pursuing research for Ph.D. degree and one post-doctoral fellow in the department. The department has also been imparting project training and internships to selected eligible undergraduate and postgraduate students from different universities.

The department has various dedicated sections that function to carry out Routine (Diagnostic) and Research activities as listed below

Diagnostic Serology Division:

The Diagnostic Serology Division of the Department provides routine clinical testing services required for clinical trials and other research studies. This is the central specimen processing unit of the department where samples are received and processed in a methodical way. The lab undertakes diagnostic testing for HIV-1 and 2, Hepatitis B and C, HSV- 2, syphilis, crypto, toxo infections. The lab is equipped with a Mindray BC- 5150 five part Hematology analyzer that fully automates the Complete Blood Count (CBC) testing. A Standardized Manual Differential Staining and Counting methodology is also in place for verifying doubtful results and samples yielding abnormal DC values. The section is equipped with a Beckton Dickinson's FACS Count System, which is used extensively to estimate absolute counts and percentages of CD4 T lymphocytes to guide treatment decision for HIV-infected patients, stage progression of Virology & Biotechnology, and assess patient prognosis

 

 

Molecular Diagnostic Division:

Since inception, this laboratory has been providing services of molecular diagnosis of HIV-1 infection and quantification of circulating virus for monitoring response to antiretroviral treatment in HIV-1-infected individuals enrolled in various clinical trials and research studies carried out at NIRT. Besides, it has been serving as a Regional Reference laboratory for molecular diagnosis of HIV infection in infants known to be exposed to HIV infection, and viral load estimation in HIV-infected individuals on ART for the National AIDS Control Organization (NACO) since 2009. The lab is implementing the advanced method of “real time PCR” in full time, with a fully automated process of RNA extraction, PCR amplification and detection. The high-end FDA approved technology “M2000sp/ M2000rt” developed by Abbott Molecular Technologies is employed to increase the sensitivity and throughput of the laboratory and improvement in turn-around-time (TAT).

Blood Lab:

The Blood Lab is equipped with a Class II Biosafety cabinet, water bath, 2 refrigerated centrifuges, and two light microscopes. This division supports vaccine immunogenicity studies and is extensively used to carry out cellular assays, multiplex ELISA, sample preparation for flow cytometric analysis and whole blood processing for other research applications. The major contribution of this division is Peripheral Blood Mononuclear Cell, neutrophil and monocyte isolation from whole blood for research as well as long term storage. The division has been serving as the in-country EQA provider for isolation and cryopreservation of PBMCs (the first and only in country PBMC EQA program) for the RePORT India Consortium since 2017.

 

 

Cell Culture Laboratory:

The Cell Culture Laboratory is equipped with two Class II Biosafety cabinets fitted with virus burn out, CO2 incubator, refrigerated multipurpose centrifuge, water bath, inverted microscope and other amenities required for research applications such as PBMC co-culture, cell line maintenance, virus (HIV) culture, anti-viral activity testing, virus neutralization assay, viral inhibition assay, etc.

Molecular Biology Lab:

The molecular biology lab is well designed to ensure unidirectional workflow in order to prevent cross-contamination. There are four dedicated rooms – Pre-PCR room, Extraction room, Amplification Room and Post-PCR room connected through a clean corridor. Differential air pressure is maintained in each room to ensure containment and prevent contamination. The facility is equipped with a dead air box in the reagent preparation area, three dedicated Class II Biosafety cabinets in the extraction area and a dedicated laminar flow hood and a Bio Rad XR Gel documentation System in the Post PCR area. Other amenities include dedicated freezers and refrigerators for storing processed and unprocessed samples and amplified PCR products, dry incubators, dry baths, refrigerated centrifuges tailor-made for various purposes, electrophoresis units, thermal cyclers for continuous throughput and Real Time- PCR systems. The infrastructure along with the trained staff is capable of providing technical support for specialized molecular biology applications.

 

 

Sanger Sequencing Facility:

This facility undertakes HIV drug resistance testing through genotyping. The lab is equipped with an Applied Biosystems 3500 Genetic Analyser. The lab was accredited by WHO in 2007 as a National Reference Laboratories for HIV-1 drug resistance genotyping to support WHO drug resistance surveillance activities and National programs for monitoring HIV drug resistance in India. The facility is also used extensively for pharmacogenetic studies aimed at identifying gene polymorphisms associated with anti- TB and anti- HIV drug metabolism through direct sequencing.

Flow Cytometry Facility:

This facility is equipped with a state-of-the-art flow cytometer cum sorter: FACS ARIA III (SORP). This instrument has the capacity to detect 11 different fluorochromes in a single tube.  It can also sort the cells of interest with high purity. The facility has contributed extensively to various cellular immunology based research studies of NIRT including the ongoing ITRC TB Vaccine Trial. The facility has been utilized by researchers from various academic and research institutions in the city for an unlimited breadth of applications.

 

 

Central TB Biorepository:

The Central Biorepository was established in 2016 at the ICMR-National Institute for Research in Tuberculosis (ICMR-NIRT), Chennai, with support from the Department of Biotechnology, to support the activities of the RePORT India Consortium. The Central TB Biorepository receives, stores and disseminates high quality biospecimens with well characterized data to support path- breaking research in tuberculosis. The Biological specimens collected at the different RePORT India clinical research sites across India from longitudinal cohorts of active TB patients and their household contacts are shipped to the Central Biorepository. The Biorepository receives and stores these biospecimens at appropriate temperatures following best practices. Different types of samples like Mycobacterium tuberculosis isolates, whole blood for RNA, whole blood for DNA, quantiferon supernatants, saliva, urine, plasma and PBMCs are stored in the Central Biorepository. The repository has 6 Ultra low deep freezers and 2 large Liquid Nitrogen Storage systems for appropriate storage of bio specimens. All storage equipment are connected to real time temperature monitoring devices. Chain of custody and inventory management at the Biorepository are implemented through the cloud- based Freezer Pro Specimen Management System. The facility is access- controlled, equipped will all safety devices as well as a dedicated generator.

Services:

i) The department has been serving as a Regional Reference Laboratory for the National AIDS Control Organization (NACO) for two National Programs viz. ‘Early Infant Diagnosis Program' and ‘Second Line ART Program'.
ii) The department is recognized as a National Reference Laboratory for WHO for HIV-1 Drug Resistance Genotyping.  
iii) The department was approved by ICMR for COVID testing in April 2020 and started COVID- 19 testing by RT- PCR in May 2020. The lab extended its testing services to Chennai Corporation during the first and second wave.
iv) The department has been serving as one of 4 ICMR- Central Depots for COVID- 19 in the country.
v) The department has been implementing the first and only in- country PBMC EQA program in the country since 2017.

 

Ongoing Research Activities

  • Cohorts for HIV Resistance and Progression in Indian Children and Adults (CoHRPICA)/ National HIV Cohort Program
  • Identification of biomarkers for predicting progression from Latent Tuberculosis Infection to Active Tuberculosis disease
  • Impact of malnutrition on immune responses to tuberculosis in Indian Children
  • Molecular and immune profiling in adults affected with COVID-19 disease
  • Development and validation of a diagnostic kit for early detection of Human Papilloma Virus (HPV) infection in cervical cancer
  • Role of Neutrophils and Neutrophil extracellular traps in the pathogenesis of Pulmonary Tuberculosis and COVID-19 co-infection
  • HL20: NIRT PBMC Cryopreservation Proficiency Testing Program
  • Impact of HIV infection and antiretroviral therapy on biomarkers for premature onset of aging-associated disorders in HIV-infected individuals
  • Construction and characterization of Infectious Molecular Clones (IMCs) of Transmitted/Founder (T/F) HIV-1 viruses
  • Introduction and characterization of point mutation in gag region of HIV-1  using Adenosine Deaminase acting on RNA (ADAR)
  • Isolation and characterization of broadly neutralizing antibodies from HIV-1 elite neutralizers.
  • Role of persistent immune activation and systemic inflammation on accelerated immune senescence and increased mortality in cured TB patients.

 


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