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Background <p>Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that has caused multiple widespread outbreaks and poses a significant public health threat. Recently, CHIKV outbreaks were reported in Guangdong Province, China. However, genomic data and information on local transmission remain limited.</p> Methods <p>We collected 19 CHIKV-positive samples from Guangzhou and carried out whole-genome sequencing via the Oxford Nanopore platform. The obtained sequences were subjected to mutational and phylogenetic analysis. Furthermore, amino acid substitutions during transmission were analyzed via DynaMut2 to assess their potential effects on protein stability.</p> Results <p>Phylogenetic analysis revealed that all 19 isolates belonged to the East/Central/South African (ECSA) lineage and were closely related to the S27b03 strain (GenBank accession: PV685524.1) from Réunion Island. Compared with S27b03, all the isolates carried a c.3879&#xa0;C &gt; T substitution. Following subsequent transmission, an additional c.7434G &gt; A substitution appeared in ten isolates. Several nonsynonymous mutations were detected, including p.G230R, p.R491Q, and p.Q528L in nsP1; p.V587M in nsP2; p.A180T in nsP4; p. I54V in E2; p.A47V in 6&#xa0;K; and p.V220A in E1. Structural prediction via DynaMut2 revealed that nsP1-G230R, nsP4-A180T, 6&#xa0;K-A47V, E1-V220A, and E2-I54V decreased protein stability (ΔΔG ≤ -0.5&#xa0;kcal/mol).</p> Conclusions <p>Our results indicate that CHIKV isolates from Guangzhou belong to the ECSA lineage and are genetically close to the S27b03 strain. During local transmission, gene mutations and amino acid substitutions are observed. These findings provide useful information for understanding CHIKV spread and may help improve surveillance and control efforts.</p>

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Genomic characterization and evolutionary analysis of Chikungunya virus strains in Guangzhou, China, 2025

  • 期刊论文

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  • 发表日期：

    2025年12月19日

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  • Yi Zhang,
  • Zhangpeng Zhuo,
  • Yanping Huang,
  • Xiuyin Zhong,
  • Xuman Mo,
  • Liying Li,
  • Qingsheng Chen

摘要

Background

Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that has caused multiple widespread outbreaks and poses a significant public health threat. Recently, CHIKV outbreaks were reported in Guangdong Province, China. However, genomic data and information on local transmission remain limited.

Methods

We collected 19 CHIKV-positive samples from Guangzhou and carried out whole-genome sequencing via the Oxford Nanopore platform. The obtained sequences were subjected to mutational and phylogenetic analysis. Furthermore, amino acid substitutions during transmission were analyzed via DynaMut2 to assess their potential effects on protein stability.

Results

Phylogenetic analysis revealed that all 19 isolates belonged to the East/Central/South African (ECSA) lineage and were closely related to the S27b03 strain (GenBank accession: PV685524.1) from Réunion Island. Compared with S27b03, all the isolates carried a c.3879 C > T substitution. Following subsequent transmission, an additional c.7434G > A substitution appeared in ten isolates. Several nonsynonymous mutations were detected, including p.G230R, p.R491Q, and p.Q528L in nsP1; p.V587M in nsP2; p.A180T in nsP4; p. I54V in E2; p.A47V in 6 K; and p.V220A in E1. Structural prediction via DynaMut2 revealed that nsP1-G230R, nsP4-A180T, 6 K-A47V, E1-V220A, and E2-I54V decreased protein stability (ΔΔG ≤ -0.5 kcal/mol).

Conclusions

Our results indicate that CHIKV isolates from Guangzhou belong to the ECSA lineage and are genetically close to the S27b03 strain. During local transmission, gene mutations and amino acid substitutions are observed. These findings provide useful information for understanding CHIKV spread and may help improve surveillance and control efforts.