Genomic characterization, transcriptome analysis, and pathogenicity of the Nipah virus (Indian isolate)

Figures & data

Table 1. The percent nucleotide and amino acid identity of the NiV isolates with NiV-M reference isolate (NC002728).

	NC002728	JN808857	MK673592	MK673585	MK673576	FJ513078	AY988601	MK673568	MK673589	MH523642	AJ564623	AY029768	AF212302
Nucleotide identity
NC002728	100.00	91.62	91.48	91.52	91.46	91.62	91.74	91.67	91.44	91.39	99.98	99.99	100.00
JN808857	91.62	100.00	99.58	99.65	99.48	99.56	99.13	99.03	98.79	97.75	91.61	91.61	91.62
MK673592	91.48	99.58	100.00	99.75	99.50	99.41	98.99	99.05	98.85	97.65	91.47	91.47	91.48
MK673585	91.52	99.65	99.75	100.00	99.47	99.49	99.06	99.02	98.80	97.73	91.51	91.51	91.52
MK673576	91.46	99.48	99.50	99.47	100.00	99.51	98.92	98.98	98.75	97.58	91.45	91.45	91.46
FJ513078	91.62	99.56	99.41	99.49	99.51	100.00	99.17	99.06	98.82	97.71	91.61	91.61	91.62
AY988601	91.74	99.13	98.99	99.06	98.92	99.17	100.00	99.66	99.42	97.86	91.73	91.73	91.74
MK673568	91.67	99.03	99.05	99.02	98.98	99.06	99.66	100.00	99.51	97.81	91.66	91.66	91.67
MK673589	91.44	98.79	98.85	98.80	98.75	98.82	99.42	99.51	100.00	97.60	91.43	91.43	91.44
MH523642	91.39	97.75	97.65	97.73	97.58	97.71	97.86	97.81	97.60	100.00	91.38	91.38	91.39
AJ564623	99.98	91.61	91.47	91.51	91.45	91.61	91.73	91.66	91.43	91.38	100.00	99.97	99.98
AY029768	99.99	91.61	91.47	91.51	91.45	91.61	91.73	91.66	91.43	91.38	99.97	100.00	99.99
AF212302	100.00	91.62	91.48	91.52	91.46	91.62	91.74	91.67	91.44	91.39	99.98	99.99	100.00
Amino acid identity
NC002728	100.00	83.61	83.38	83.42	83.40	83.68	83.86	83.76	83.37	83.25	99.97	99.97	100.00
JN808857	83.61	100.00	99.18	99.26	99.13	99.16	98.22	98.09	97.67	95.30	83.60	83.58	83.61
MK673592	83.38	99.18	100.00	99.52	99.06	98.93	98.01	98.04	97.65	95.17	83.37	83.35	83.38
MK673585	83.42	99.26	99.52	100.00	99.05	99.01	98.09	98.03	97.63	95.25	83.40	83.38	83.42
MK673576	83.40	99.13	99.06	99.05	100.00	99.18	97.98	98.01	97.60	95.12	83.38	83.37	83.40
FJ513078	83.68	99.16	98.93	99.01	99.18	100.00	98.42	98.26	97.83	95.28	83.66	83.65	83.68
AY988601	83.86	98.22	98.01	98.09	97.98	98.42	100.00	99.47	99.01	95.56	83.84	83.83	83.86
MK673568	83.76	98.09	98.04	98.03	98.01	98.26	99.47	100.00	99.08	95.51	83.74	83.73	83.76
MK673589	83.37	97.67	97.65	97.63	97.60	97.83	99.01	99.08	100.00	95.13	83.35	83.33	83.37
MH523642	83.25	95.30	95.17	95.25	95.12	95.28	95.56	95.51	95.13	100.00	83.23	83.22	83.25
AJ564623	99.97	83.60	83.37	83.40	83.38	83.66	83.84	83.74	83.35	83.23	100.00	99.93	99.97
AY029768	99.97	83.58	83.35	83.38	83.37	83.65	83.83	83.73	83.33	83.22	99.93	100.00	99.97
AF212302	100.00	83.61	83.38	83.42	83.40	83.68	83.86	83.76	83.37	83.25	99.97	99.97	100.00

Figure 1. Characterization of NiV in cells: Growth kinetics in the Vero (ATCC® CCL − 81™) cells expressed in a) TCID50 and b) viral RNA copy number/ml. c) Vero CCL − 81 cells showing cytopathic effects after 1 day post NiV infection, and d)cell control. Differential expression of NiV genes in e) Vero-CCL81 cells expressed as RPKM values at different time points. f) BHK − 21 cells infected with NiV showing cytopathic effect on 3 days post infection and g) BHK − 21 cell control. Differential expression of NiV genes in h) BHK − 21 cells expressed as RPKM values at different time points.

Figure 2. Survival and body weight changes in hamsters after NiV infection. a) Percent survival and b) body weight change in hamsters post intraperitoneal infection. c) Percent survival and d) body weight change in hamsters post intranasal infection.

Figure 3. NiV RNA shedding and viremia in hamsters post intraperitoneal infection. a) Viral shed through the nasal wash, oral and rectal route. b) Viral RNA in serum samples collected from hamsters on various time points. The individual values along with median value are plotted in the graph.

Figure 4. NiV load in organs of hamsters after intraperitoneal infection. Viral RNA load in a) brain b) heart c) lungs d) trachea e) intestine f) spleen g) liver and h) kidney. i) Live virus load in brain, lungs, spleen and kidney. The individual values along with median value are plotted in the graph.

Figure 5. Histopathological observations in NiV infected hamsters after intraperitoneal infection. a) Lung section showing multifocal perivascular inflammatory cell infiltration in the alveolar parenchyma (arrows) on 3 days post infection, (H& E, scale bar = 100 µm). b) Lung section showing vasculitis, thrombosis and diffuse alveolar thickening on 7 days post infection, (H& E, scale bar = 100 µm) c) Blood vessel in the lungs showing multiple endothelial cell syncitia formation (arrows) and perivascular mononuclear cell infiltration, (H& E, scale bar = 200 µm) d) Lung section showing normal histological features, (H& E, scale bar = 200 µm) e) Brain section showing blood vessels with haemorrhage in the perivascular space, (H& E, scale bar = 200 µm). f) Brain section showing multiple blood vessels with perivascular cuffing, (H& E, scale bar = 100 µm). g) Brain section showing blood vessels with perivascular cuffing (yellow arrows) and gliosis (red arrow), (H& E, scale bar = 200 µm). h) Brain section showing normal histological features, (H& E, scale bar = 100 µm) i) Kidney section showing diffuse vascular engorgement, (H& E, scale bar = 200 µm).J) Kidney section showing congested blood vessels and thrombotic plugs in the glomerular capillaries, (H& E, scale bar = 200 µm).K) Kidney section showing normal histological features, (H& E, scale bar = 100 µm).

Figure 6. Host gene expression in hamsters after intraperitoneal NiV infection. Fold change of A) IL − 1 B) IL − 4 C) IL − 6 D) IL − 10 E) IL − 12 and F) IFN- γ in brain, lungs, and spleen. The individual values along with median value are plotted in the graph.

Figure 7. Viral RNA load in hamsters post intranasal NiV infection. A) Viral RNA shed through the nasal wash, oral and rectal route. Viral RNA in B) lungs c) liver d) heart e) intestine f) kidney and spleen samples collected from hamsters on various time points. The individual values along with median value are plotted in the graph.

Data Availability statement

The authors confirm that the data supporting the findings of this study are available within the article. The transcriptome data that support the findings of this study are openly available in NCBI at https://www.ncbi.nlm.nih.gov/sra/?term=, reference number. [SRR24202203, SRR24202204, SRR24202205, SRR24202206, SRR24202207, SRR24202208, SRR24202209, SRR24202210, SRR24202211, SRR24202212].