OmniVira

Literature detail

Emergence and adaptive evolution of Nipah virus.

Kemang Li1 Shiyu Yan1 Ningning Wang1 Wanting He1 Haifei Guan1 Chengxi He1 Zhixue Wang1 Meng Lu1 Wei He1 Rui Ye1 Michael Veit2 Shuo Su1
Affiliations 2 institutions
  1. MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.
  2. Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Berlin, Germany.
PMID 31408582 2020 Transbound Emerg Dis eng ppublish
PubMed DOI Browse context

Article

Publication summary

Since its first emergence in 1998 in Malaysia, Nipah virus (NiV) has become a great threat to domestic animals and humans. Sporadic outbreaks associated with human-to-human transmission caused hundreds of human fatalities. Here, we collected all available NiV sequences and combined phylogenetics, molecular selection, structural biology and receptor analysis to study the emergence and adaptive evolution of NiV. NiV can be divided into two main lineages including the Bangladesh and Malaysia lineages. We formly confirmed a significant association with geography which is probably the result of long-term evolution of NiV in local bat population. The two NiV lineages differ in many amino acids; one change in the fusion protein might be involved in its activation via binding to the G protein. We also identified adaptive and positively selected sites in many viral proteins. In the receptor-binding G protein, we found that sites 384, 386 and especially 498 of G protein might modulate receptor-binding affinity and thus contribute to the host jump from bats to humans via the adaption to bind the human ephrin-B2 receptor. We also found that site 1645 in the connector domain of L was positive selected and involved in adaptive evolution; this site might add methyl groups to the cap structure present at the 5'-end of the RNA and thus modulate its activity. This study provides insight to assist the design of early detection methods for NiV to assess its epidemic potential in humans.

Adaptation, Biological Disease Outbreaks Polymorphism, Genetic Animals Bangladesh Biological Evolution Chiroptera Computational Biology Geography Henipavirus Infections Host Specificity Humans Malaysia Models, Molecular Nipah Virus Phylogeny Viral Proteins

Structured evidence records

Evidence records

8 total
Genomic Evolution 3 records
Genomic Evolution Extraction confidence 0.95
Key finding

Phylogenetic and molecular selection analyses of Nipah virus sequences revealed two main lineages, Bangladesh and Malaysia, reflecting long-term geographical evolution in bat populations.

Virus
NiV
Host
Chiroptera
Location
Not specified
Supporting text

Here, we collected all available NiV sequences and combined phylogenetics, molecular selection, structural biology and receptor analysis to study the emergence and adaptive evolution of NiV. NiV can be divided into two main lineages including the Bangladesh and Malaysia lineages.

Analysis methods
phylogenetics; molecular selection analysis
Genomic Evolution Extraction confidence 0.95
Key finding

Sequence analysis identified adaptive sites in the G protein, notably position 498, potentially mediating Nipah virus adaptation from bats to humans by altering ephrin-B2 receptor binding.

Virus
NiV
Location
Not specified
Supporting text

In the receptor-binding G protein, we found that sites 384, 386 and especially 498 of G protein might modulate receptor-binding affinity and thus contribute to the host jump from bats to humans via the adaption to bind the human ephrin-B2 receptor.

Genes or proteins
G protein
Analysis methods
molecular selection analysis
Genomic Evolution Extraction confidence 0.90
Key finding

Positive selection was detected at site 1645 in the L protein, suggesting adaptive evolution that may influence RNA capping activity.

Virus
NiV
Host
Not specified
Location
Not specified
Supporting text

We also found that site 1645 in the connector domain of L was positive selected and involved in adaptive evolution; this site might add methyl groups to the cap structure present at the 5'-end of the RNA and thus modulate its activity.

Genes or proteins
L protein
Analysis methods
molecular selection analysis
Molecular Adaptation 3 records
Molecular Adaptation Extraction confidence 0.98
Key finding

Amino acid substitutions in the Nipah virus G protein, particularly at site 498, may enhance binding to the human ephrin-B2 receptor and facilitate adaptation from bats to humans.

Virus
NiV
Host
Not specified
Location
Not specified
Supporting text

In the receptor-binding G protein, we found that sites 384, 386 and especially 498 of G protein might modulate receptor-binding affinity and thus contribute to the host jump from bats to humans via the adaption to bind the human ephrin-B2 receptor.

Genes or proteins
G protein
Receptors
human ephrin-B2 receptor
Mutations
site 384; site 386; site 498
Mechanism types
receptor_binding; host_range_adaptation
Molecular Adaptation Extraction confidence 0.95
Key finding

A positively selected site at position 1645 in the Nipah virus L protein may influence RNA capping activity and contribute to viral adaptive evolution.

Virus
NiV
Host
Not specified
Location
Not specified
Supporting text

We also found that site 1645 in the connector domain of L was positive selected and involved in adaptive evolution; this site might add methyl groups to the cap structure present at the 5'-end of the RNA and thus modulate its activity.

Genes or proteins
L protein
Mutations
site 1645
Mechanism types
replication_efficiency; polymerase_activity
Molecular Adaptation Extraction confidence 0.90
Key finding

An amino acid change in the Nipah virus fusion protein may affect its activation through interaction with the G protein, reflecting adaptive divergence between Malaysian and Bangladesh lineages.

Virus
NiV
Host
Not specified
Location
Not specified
Supporting text

The two NiV lineages differ in many amino acids; one change in the fusion protein might be involved in its activation via binding to the G protein.

Genes or proteins
fusion protein; G protein
Mechanism types
protein_interaction; pathogenicity
Receptor Usage 1 records
Receptor Usage Extraction confidence 0.90
Key finding

Amino acid sites 384, 386, and 498 in the G protein of Nipah virus modulate receptor-binding affinity and facilitate adaptation to the human ephrin-B2 receptor, supporting receptor-mediated host jump from bats to humans.

Virus
NiV
Location
Not specified
Supporting text

In the receptor-binding G protein, we found that sites 384, 386 and especially 498 of G protein might modulate receptor-binding affinity and thus contribute to the host jump from bats to humans via the adaption to bind the human ephrin-B2 receptor.

Method
structural biology; receptor analysis
Receptors
ephrin-B2 receptor
Spillover Event 1 records
Spillover Event Extraction confidence 0.80
Key finding

Adaptive changes in the Nipah virus G protein are proposed to have enabled cross-species transmission from bats to humans through enhanced binding to the human ephrin-B2 receptor.

Virus
NiV
Location
Not specified
Supporting text

Sites 384, 386 and especially 498 of the Nipah virus G protein might modulate receptor-binding affinity and thus contribute to the host jump from bats to humans via the adaption to bind the human ephrin-B2 receptor.

Method
phylogenetics; molecular selection analysis; structural biology; receptor analysis
Study design
phylogenetic analysis
Transmission direction
animal-to-human