Genomic conservation and CNS-associated intra-host variation of Nipah virus during the 1998-1999 Malaysian outbreak.

Authors

Heng Choon Cheong, Foo Hou Tan, Hui Ming Ong, Kum Thong Wong, Kien Chai Ong, Soon Hao Tan, Chong Tin Tan, Li Ping Wong, Jie Ping Schee, Rozainanee Mohd-Zain, Aziyah Mat Rahim, Nuryana Idris, Kok Keng Tee, Li-Yen Chang

Published in

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases. Pages 108894. Jun 19, 2026. Epub Jun 19, 2026.

Abstract

Nipah virus (NiV) is a highly pathogenic henipavirus responsible for recurrent outbreaks of severe encephalitis. This study aimed to address gaps in historical genomic data by characterizing NiV genomes recovered from archived central nervous system (CNS) tissues from the 1998-1999 Malaysian outbreak and evaluating viral evolution and intra-host genetic variation.
We analyzed 18 NiV genomes obtained from archived CNS tissues. Whole-genome sequencing was performed, followed by phylogenetic reconstruction, comparative genomic analysis, and intra-host single nucleotide variant (iSNV) profiling. Paired CNS tissue samples from the individual patients were included to assess regional viral heterogeneity across distinct CNS tissues.
All Malaysian NiV sequences formed a highly conserved, monophyletic clade (NiV-MY), distinct from the Bangladesh-India lineage (NiV-BD). Overall genomic diversity was low, with high amino acid conservation across the genome. Although intra-host variation was limited, however, paired CNS tissue samples from two patients contained closely related but non-identical genomes, differing by a single nucleotide in the attachment glycoprotein (G) gene, indicating localized genetic variation across distinct CNS tissues.
NiV from the Malaysian outbreak demonstrated remarkable genomic conservation consistent with a single dominant introduction or a highly restricted set of closely related introductions. Nevertheless, the presence of limited intra-host variation highlights ongoing micro-evolution within the CNS and underscores the importance of continued genomic surveillance to better understand NiV evolutionary dynamics.

PMID:
42320843
Bibliographic data and abstract were imported from PubMed on 20 Jun 2026.

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