Investigator(s)
| WHO Technical Officer |
Lucky Sangal WHO SEARO -IVD Lucky Sangal 
|
| Principal Investigator |
Lucky Sangal WHO SEARO -IVD Lucky Sangal
|
Title(s) and abstract
| Scientific title | Validation of direct detection nanopore sequencing-based method for identification of poliovirus in South-East Asia Region |
| Public title | Validation of DDNS for poliovirus |
| Background | With the changing epidemiology of poliovirus in the South-East Asia region, the region needs to adopt sensitive laboratory methods with rapid turnaround times. Direct Detection through Nanopore Sequencing (DDNS) is one such method. DDNS also allows the detection of other pathogens causing Acute Flaccid Paralysis (AFP), specifically non-poliovirus enteroviruses. As the conventional methods have been standardized and used globally in WHO-accredited laboratories that are part of the Global Polio Laboratory Network (GPLN), it is crucial to generate evidence that DDNS performs at par or better than the conventional methods. To validate the use of DDNS in AFP and environmental surveillance of polioviruses, the proposed study has selected four polio laboratories from different geographical regions of South-East Asia. As a part of this study, the staff from these laboratories will be trained in DDNS. The selected laboratories will parallelly test the AFP and environmental samples using conventional methods and DDNS. The results will then be analyzed to validate DDNS as an alternative to conventional methods. The project will also explore using nanopore sequencing as a molecular epidemiolog |
| Objectives | General Objective: This study aims to validate and assess feasibility and cost effectiveness of nanopore sequencing-based methods in detecting and characterizing poliovirus in AFP and environmental surveillance. Specific Objectives: The specific objectives of the proposed project are as follows. 1. Comparative validation of DDNS for stool samples. Validation of DDNS method for poliovirus detection in stool specimens of clinically suspected AFP cases and comparison of results with the conventional method. 2. Comparative validation of DDNS for wastewater samples. Validation of DDNS method for poliovirus detection in wastewater specimens and comparison of results with the conventional method. 3. Comparative validation of DDNS for intratypic differentiation of poliovirus. Validation of VP1 sequencing using poliovirus isolates from the conventional method. 4. Utility of whole-genome sequencing as a molecular epidemiology tool. Using nanopore sequencing to evaluate whole-genome sequencing as a poliovirus and non-polio enteroviruses molecular epidemiology tool. |
| Study Methods | The proposed study is an experimental study for validating the novel DDNS method by comparing it with the conventional method in parallel testing. 1. Capacity building and resource mobilization: Selection of polio laboratories from SEAR for the study, capacity assessment and distribution of non-consumable and consumable resources, hands-on training. 2. Sample testing: testing of Acute Flaccid Paralysis and environmental samples for polioviruses using conventional method and DDNS. 3. Validation studies: Agreeability, sensitivity and specificity analysis 4. Cost-effectiveness study: Multiple criteria decision making (MCDA) model using simple additive weighting (SAW) |
| Expected outcomes and use of results | Expected Outcomes: 1. Validation of DDNS method for poliovirus and NPEV detection in AFP stool samples and environmental samples. 2. Validation of nanopore sequencing for intratypic differentiation of polioviruses. 3. Utility of DDNS method for detection of non-polio enteroviruses. 4. Utility of nanopore sequencing for whole genome sequencing of polioviruses. Use of results: DDNS DDNS method has several advantages over the conventional method [3, 4]– 1. Rapid turnaround time. results within seven days of receiving the sample as compared to conventional protocol where negative samples are detected in 14 days with further 20 says required for obtaining sequencing results. 2. Handling mixed samples. DDNS can handle samples with multiple pathogens present making it a good alternative for environmental surveillance. |
| Keywords | poliovirus, detection, environmental surveillance, AFP surveillance, DDNS, intratypic differentiation, ITD, sequencing |
Research Details
| Student research | No |
| Start Date | 01-Nov-2024 |
| End Date | 01-Nov-2026 |
| Key Implementing Institution | Self |
| Multi-country research | Yes |
| India, Indonesia, Thailand | |
| Nationwide research | No |
| India, Indonesia, Indonesia, Thailand | |
| Research Domain(s) | Communicable Disease Research |
| Research field(s) | Immunization/Vaccine Preventable Disease |
| Involves human subjects | No |
| Data Collection | Secondary data |
| Proposal reviewed by other Committee | No |