Whole-genome sequencing and genetic characterization of norovirus from diarrhea patients in Tongling City

doi:10.20199/j.issn.1672-2302.2026.04.009

Abstract

Abstract:

ObjectiveTo investigate the genetic characteristics of norovirus (NoV) from diarrhea patients in Tongling area for scientific evidence in prevention and control of this infection. Methods Three NoV-positive fecal samples (designated NR18, NR61, and NR246) were collected from diarrhea patients treated at medical institutions in Tongling City in 2023. Viral RNA was extracted and subjected to high-throughput sequencing. The obtained whole-genome sequences were uploaded to the NCBI database for BLAST homology alignment to identify their genotypes. Then a phylogenetic tree was constructed using MEGA 11 software, and closely related reference strains were selected based on evolutionary clades. Sequence homology analysis was performed using BioEdit software on the three viral strains and a reference strain, and amino acid mutation sites in the capsid proteins VP1 and VP2 regions were identified. Results The whole-genome length of NR18, NR61, and NR246 was 7 641 nt, 7 784 nt and 7 567 nt, respectively. Genotyping and phylogenetic analysis revealed that NR18 belonged to genotype GⅠ.4 P4 and clustered with the Guangdong isolate PV640830.1, NR61 was classified as GⅠ.2 P2 and grouped with the Japanese isolate LC122690.1, NR246 was identified as GⅡ.6 P7 and clustered with the Shaanxi isolate MW243610.2. Homology analysis demonstrated high sequence similarity between the three strains and their corresponding reference strains (nucleotide identity in ORF regions ranged from 95.3% to 99.7%, and amino acid identity in VP regions from 93.5% to 99.5%). Amino acid mutation analysis showed that NR61 exhibited the most pronounced variation, with 27 and 8 mutation sites in the VP1 and VP2 regions, respectively, relative to its reference strain, followed by NR246, with 15 and 8 mutation sites. NR18 was the most conserved, with only 8 and 1 mutation sites in VP1 and VP2, respectively. Conclusion NoV strains in Tongling City exhibited genetic diversity, with varying degrees of amino acid mutations in the VP1 and VP2 regions. It is recommended to implement routine dynamic monitoring of NoV whole-genome sequences to track viral evolution and mutation patterns of the virus, providing insights for regional NoV prevention and control.

Key words: Norovirus, Whole-genome sequence, Phylogenetic analysis, Amino acid mutation

CLC Number:

R373.2

WANG Yuanyuan, ZUO Yancai, LIU Xiaosong, QIU Shenwei, HUANG Li, CUI Hongjuan, PAN Kai. Whole-genome sequencing and genetic characterization of norovirus from diarrhea patients in Tongling City[J]. Journal of Tropical Diseases and Parasitology, 2026, 24(4): 236-240.

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序列区域	NR18	NR61	NR246
全长	7 641	7 784	7 567
ORF1	1~5 319	1~5 371	1~5 095
ORF2	5 306~6 940	5 355~6 995	5 079~6 731
ORF3	6 940~7 566	6 995~7 630	6 731~7 510

毒株	LC122690.1			MW243610.2			PV640830.1			NR18			NR246			NR61
毒株	ORF1	ORF2	ORF3	ORF1	ORF2	ORF3	ORF1	ORF2	ORF3	ORF1	ORF2	ORF3	ORF1	ORF2	ORF3	ORF1	ORF2	ORF3
LC122690.1	100.0	100.0	100.0	37.9	36.9	32.6	70.5	67.2	62.1	70.5	67.1	62.2	38.3	37.0	32.5	98.7	98.2	98.7
MW243610	37.9	36.9	32.6	100.0	100.0	100.0	38.1	38.0	30.3	38.2	37.9	30.0	98.7	98.9	95.3	38.0	36.7	32.7
PV640830.1	70.5	67.2	62.1	38.1	38.0	30.3	100.0	100.0	100.0	99.7	99.3	99.6	38.2	38.0	31.6	70.3	67.3	62.4
NR18	70.5	67.1	62.2	38.2	37.9	30.0	99.7	99.3	99.6	100.0	100.0	100.0	38.3	37.8	31.4	70.3	67.3	62.5
NR246	38.3	37.0	32.5	98.7	98.9	95.3	38.2	38.0	31.6	38.3	37.8	31.4	100.0	100.0	100.0	38.3	36.8	32.6
NR61	98.7	98.2	98.7	38.0	36.7	32.7	70.3	67.3	62.4	70.3	67.3	62.5	38.3	36.8	32.6	100.0	100.0	100.0

毒株	LC122690.1		MW243610.2		PV640830.1		NR18		NR246		NR61
毒株	VP1	VP2	VP1	VP2	VP1	VP2	VP1	VP2	VP1	VP2	VP1	VP2
LC122690.1	100.0	100.0	12.9	11.8	51.5	51.5	51.2	52.0	13.1	11.6	96.3	97.5
MW243610	12.9	11.8	100.0	100.0	12.4	10.4	12.2	10.0	97.9	93.5	12.4	11.5
PV640830.1	51.5	51.5	12.4	10.4	100.0	100.0	98.8	99.5	12.6	11.4	52.2	52.0
NR18	51.2	52.0	12.2	10.0	98.8	99.5	100.0	100.0	12.4	11.0	51.9	52.5
NR246	13.1	11.6	97.9	93.5	12.6	11.4	12.4	11.0	100.0	100.0	12.6	11.2
NR61	96.3	97.5	12.4	11.5	52.2	52.0	51.9	52.5	12.6	11.2	100.0	100.0

突变位点	52	64	79	86	125	136	141	157	194	203	205	210	226	229	249	254	291	294	295	331	332	364	398	406	411	496	517	81^*	100^*	125^*	129^*	152^*	160^*	168^*	175^*
NR61	F	I	T	I	P	S	Q	V	S	A	T	F	P	L	L		V	I	L	I	I	S	G	T	C	L	I	P	D	R	V	T	S	C	P
LC122690.1	S	T	I	T	L	F	L	A	L	V	I	S	L	P	P	W	A	T	S	T	T	L	D	I	Y	P	T	L	G	C	G	I	F	Y	L

突变位点	16	31	105	109	144	152	176	294	312	317	352	366	409	419	451	42^*	92^*	152^*	178^*	216^*	230^*	246^*	259^*
NR246	N	V	W	A	S	G	A	R	Q	G	I	Q		L	P		K	A	K		A	T
MW243610.2	S	A	C	V	L	V	V	Q	R	D	T	R	W	S	L	K	R	V		Q	V	A	E