Location: Research Programs
Project Number: 3022-32000-018-067-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 1, 2026
End Date: Aug 31, 2028
Objective:
Nipah virus (NiV) is a high-consequence zoonotic pathogen with case fatality rates exceeding 70% and recurring outbreaks in South Asia, especially in Bangladesh. Despite active clinical diagnostic and wildlife surveillance efforts, viral genomic data remain critically limited, with fewer than 100 high-quality full-length genomes available in public databases (PubMed, GISAID, etc.). This lack of genomic resolution constrains detection of emerging variants, limits evaluation of vaccine-relevant antigen stability under development, and challenges outbreak response systems. Endemic and potentially endemic regions (including Bangladesh, Malaysia, Indonesia, Thailand, Bhutan, Myanmar, Nepal, etc.) with limited laboratory infrastructure, lack of standardized next-generation sequencing (NGS) workflows, and analytical pipelines are main reasons behind limited NiV genomic data availability. Additionally, there is no established protocol to integrate genomic data into global surveillance platforms such as the World Animal Health Information System (WAHIS). Our proposal aims to establish an operational, scalable genomic surveillance system for NiV that increases genomic data availability, standardizes sequencing workflows, enables reproducible research, and outbreak monitoring.
Objective 1: Expand high-quality complete NiV genomic sequences using targeted surveillance and Agnostic sequencing in endemic and at-risk regions
We will generate 20–50 full-length NiV genomes from human, bat, and livestock samples and train USDA/WOAH-affiliated staff in viral sequencing and analysis.
Outcome: Increased global genomic dataset and regional sequencing capacity.
Objective 2: Develop a De Novo NGS Workflow and portable amplicon-based sequencing platform for NiV genome recovery in low-resource settings
We will establish a standardized sequencing and analysis pipeline, including development and validation of an ARTIC-style amplicon panel optimized for low-resource settings.
Outcome: Reproducible, portable workflow for NiV genomic surveillance.
Objective 3: Establish a well-characterized NiV biorepository and integrate sequencing data with World Animal Health Information System (WAHIS)
We will develop standardized data delivery to GISAID and add to reporting pipelines linking genomic data with outbreak reporting systems.
Outcome: Enhanced outbreak tracking and decision support through genomic epidemiology.
Impact: This project delivers a practical surveillance system that directly supports vaccine evaluation, outbreak monitoring, and global preparedness.
Approach:
Objective 1: We will increase the global catalog of complete or near-complete NiV genomes (currently limited to approximately 100 high-quality entries in NCBI/Nextstrain as of early 2026) by screening and sequencing NiV-positive and NiV-like samples from our ongoing field collections. Using our established VirCapSeq-VERT capture platform, we will process previously collected bat, rodent, livestock, and human samples (including plasma and saliva from close contacts of confirmed cases to detect potential asymptomatic infections) collected in Bangladesh, with parallel efforts on Pteropus medius from Bhutan and Nepal. Routine RT-PCR–negative but clinically NiV-like human samples will be reanalyzed with VCS to recover genomes potentially missed due to primer mismatches. Positive samples will undergo complete NiV genome retrieval, mutational analysis, and antigenic drift assessment relative to existing databases to evaluate implications for vaccine effectiveness. All generated sequences will be uploaded to GISAID, NCBI GenBank, and Nextstrain. This aim directly addresses the paucity of diverse, high-quality full-length sequences needed for robust phylogenetic tracking and vaccine design, while extending our prior work on agnostic viral discovery in unexplained Nipah-like illnesses.
Objective 2: Building on VirCapSeq-VERT’s established performance for enrichment of viral sequencing (1,000–10,000-fold sensitivity) enrichment and viral genome recovery, we will optimize a standard, culture-independent de novo analysis workflow for NiV next-generation sequencing. This will include standardized protocols for RNA extraction from diverse matrices (swabs, tissues, saliva, plasma), library preparation, and bioinformatics pipelines tailored for variable viral loads typical in field samples. Based on newly recovered NiV genomes and existing genomes, we will design and validate an ARTIC-style multiplex amplicon sequencing panel compatible with Oxford Nanopore Technologies MinION. The panel will target all NiV lineages, enabling rapid, low-cost whole-genome sequencing directly in endemic countries with limited infrastructure. Development and validation will use inactivated NiV viral culture in trizol provided by UTMB, newly generated sequences plus archived positives. This objective responds to the need for equitable, real-time genomic tools in resource-constrained settings where timely sequencing can inform outbreak response.
Objective 3: We will create a centralized, accessible biorepository of NiV strains rigorously characterized by full-genome sequences of NiV. This will include bat-derived, livestock, and human isolates generated or confirmed in this project, with metadata on host, geography, collection date, and clinical context. To enable real-time monitoring, we will develop standardized operating procedures to link NiV sequencing outputs (lineage, mutations, drift signals) directly to the World Animal Health Information System (WAHIS), including automated or semi-automated data uploads from regional laboratories trained (virtually) under Aim 1. This integration will support genomic epidemiology of outbreaks, early detection of variants.