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Inference of Nipah virus evolution, 1999-2015
Shannon L M Whitmer1, Michael K Lo1, Hossain M S Sazzad2,3
1Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30329, USA.
Virus Evolution
|August 23, 2021
Summary
Nipah virus (NiV) outbreaks in Bangladesh yield limited genomic data. New methods generated 35 full genomes, revealing two distinct NiV clades with limited genetic variation, impacting public health strategies.
Area of Science:
- Virology
- Genomics
- Epidemiology
- Evolutionary Biology
Background:
- Nipah virus (NiV) causes near-annual human outbreaks in Bangladesh, primarily from bat spillover.
- Generating whole-genome NiV sequences from human samples is difficult due to low viral loads.
- Existing genomic data for NiV in Bangladesh is sparse, hindering evolutionary and epidemiological studies.
Purpose of the Study:
- To generate novel full-length Nipah virus genomic sequences from human specimens in Bangladesh.
- To investigate the temporal and geographic evolutionary history of NiV in Bangladesh.
- To enhance tools for visualizing NiV spatio-temporal spread.
Main Methods:
- Utilized targeted enrichment with custom NiV-specific probes for whole-genome sequencing.
- Generated 35 unique full-length genomic sequences directly from human specimens and viral isolates.
- Employed Bayesian continuous diffusion analysis to model spatio-temporal spread and evolutionary history.
Main Results:
- Successfully generated 35 additional unique full-length NiV genomic sequences.
- Identified two distinct NiV clades in Bangladesh that have intermingled geographically over time.
- Observed limited evidence of significant selection, with initial differentiation in the polymerase gene and subsequent mutations in other genes.
Conclusions:
- NiV in Bangladesh, despite widespread presence, exhibits limited genetic variation across its clades.
- The study highlights the need to investigate NiV genetic variation in bat populations.
- Findings suggest potential genetic bottlenecks during zoonotic transmission and the need to evaluate current surveillance methods.
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